def create_quast_config_file(experiment_id='exp001', reference_dataset_id='NONE', reference_file='NONE', assembly_dataset_id='sdnt-170101-235959', assembly_type='CONTIGS'):
'''
Create QUAST config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the app
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_star_code()):
assembly_software = xlib.get_star_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the QUAST config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_quast_config_file())):
os.makedirs(os.path.dirname(get_quast_config_file()))
with open(get_quast_config_file(), mode='w', encoding='utf8') as file_id:
file_id.write('{0}\n'.format('# You must review the information of this file and update the values with the corresponding ones to the current run.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# The reference file must be located in the cluster directory {0}/experiment_id/reference_dataset_id'.format(xlib.get_cluster_reference_dir())))
file_id.write('{0}\n'.format('# The assembly files must be located in the cluster directory {0}/experiment_id/assembly_dataset_id'.format(xlib.get_cluster_result_dir())))
file_id.write('{0}\n'.format('# The experiment_id, reference_dataset_id, reference_file and assembly_dataset_id are fixed in the identification section.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# You can consult the parameters of QUAST and their meaning in http://quast.sourceforge.net/quast.html.'))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information identifies the experiment.'))
file_id.write('{0}\n'.format('[identification]'))
file_id.write('{0:<50} {1}\n'.format('experiment_id = {0}'.format(experiment_id), '# experiment identification'))
file_id.write('{0:<50} {1}\n'.format('reference_dataset_id = {0}'.format(reference_dataset_id), '# reference dataset identification or NONE'))
file_id.write('{0:<50} {1}\n'.format('reference_file = {0}'.format(reference_file), '# reference file name or NONE'))
file_id.write('{0:<50} {1}\n'.format('assembly_software = {0}'.format(assembly_software), '# assembly software: {0} ({1}) or {2} ({3}) or {4} ({5}) or {6} ({7}) or {8} ({9}) or {10} ({11})'.format(xlib.get_soapdenovotrans_code(), xlib.get_soapdenovotrans_name(), xlib.get_transabyss_code(), xlib.get_transabyss_name(), xlib.get_trinity_code(), xlib.get_trinity_name(), xlib.get_star_code(), xlib.get_star_name(), xlib.get_cd_hit_est_code(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code(), xlib.get_transcript_filter_name())))
file_id.write('{0:<50} {1}\n'.format('assembly_dataset_id = {0}'.format(assembly_dataset_id), '# assembly dataset identification'))
file_id.write('{0:<50} {1}\n'.format('assembly_type = {0}'.format(assembly_type), '# CONTIGS or SCAFFOLDS in {0}; NONE in {1}, {2}, {3}, {4} and {5}'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name())))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information to set the QUAST parameters'))
file_id.write('{0}\n'.format('[QUAST parameters]'))
file_id.write('{0:<50} {1}\n'.format('threads = 2', '# number of threads for use'))
except:
error_list.append('*** ERROR: The file {0} can not be recreated'.format(get_quast_config_file()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def get_cd_hit_est_process_starter():
'''
Get the CD-HIT-EST process starter path in the local computer.
'''
# assign the CD-HIT-EST process starter path
cd_hit_est_process_starter = '{0}/{1}-process-starter.sh'.format(
xlib.get_temp_dir(), xlib.get_cd_hit_est_code())
# return the CD-HIT-EST starter path
return cd_hit_est_process_starter
def get_cd_hit_est_config_file():
'''
Get the CD-HIT-EST config file path.
'''
# assign the CD-HIT-EST config file path
cd_hit_est_config_file = '{0}/{1}-config.txt'.format(
xlib.get_config_dir(), xlib.get_cd_hit_est_code())
# return the CD-HIT-EST config file path
return cd_hit_est_config_file
def get_assembly_software_code_list():
'''
Get the code list of "assembly_software".
'''
return [
xlib.get_soapdenovotrans_code(),
xlib.get_transabyss_code(),
xlib.get_trinity_code(),
xlib.get_ggtrinity_code(),
xlib.get_cd_hit_est_code(),
xlib.get_transcript_filter_code()
]
def execute(self, event=None):
'''
Execute the list the result logs in the cluster.
'''
# validate inputs
OK = self.validate_inputs()
if not OK:
message = 'Some input values are not OK.'
tkinter.messagebox.showerror('{0} - {1}'.format(xlib.get_project_name(), self.head), message)
# get the run dictionary of the experiment
if OK:
# -- command = 'ls {0}/{1}'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get())
command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get())
(OK, stdout, stderr) = xssh.execute_cluster_command(self.ssh_client, command)
if OK:
result_dataset_dict = {}
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id = line
try:
pattern = r'^(.+)\-(.+)\-(.+)$'
mo = re.search(pattern, result_dataset_id)
bioinfo_app_code = mo.group(1).strip()
yymmdd = mo.group(2)
hhmmss = mo.group(3)
date = '20{0}-{1}-{2}'.format(yymmdd[:2], yymmdd[2:4], yymmdd[4:])
time = '{0}:{1}:{2}'.format(hhmmss[:2], hhmmss[2:4], hhmmss[4:])
except:
bioinfo_app_code = 'xxx'
date = '0000-00-00'
time = '00:00:00'
if result_dataset_id.startswith(xlib.get_bedtools_code()+'-'):
bioinfo_app_name = xlib.get_bedtools_name()
elif result_dataset_id.startswith(xlib.get_blastplus_code()+'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_bowtie2_code()+'-'):
bioinfo_app_name = xlib.get_bowtie2_name()
elif result_dataset_id.startswith(xlib.get_busco_code()+'-'):
bioinfo_app_name = xlib.get_busco_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_est_code()+'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_detonate_code()+'-'):
bioinfo_app_name = xlib.get_detonate_name()
elif result_dataset_id.startswith(xlib.get_emboss_code()+'-'):
bioinfo_app_name = xlib.get_emboss_name()
elif result_dataset_id.startswith(xlib.get_fastqc_code()+'-'):
bioinfo_app_name = xlib.get_fastqc_name()
elif result_dataset_id.startswith(xlib.get_gmap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_name()
elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code()+'-'):
bioinfo_app_name = xlib.get_gmap_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gzip_code()+'-'):
bioinfo_app_name = xlib.get_gzip_name()
elif result_dataset_id.startswith(xlib.get_insilico_read_normalization_code()+'-'):
bioinfo_app_name = xlib.get_insilico_read_normalization_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code()+'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_ngshelper_code()+'-'):
bioinfo_app_name = xlib.get_ngshelper_name()
elif result_dataset_id.startswith(xlib.get_quast_code()+'-'):
bioinfo_app_name = xlib.get_quast_name()
elif result_dataset_id.startswith(xlib.get_r_code()+'-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(xlib.get_ref_eval_code()+'-'):
bioinfo_app_name = xlib.get_ref_eval_name()
elif result_dataset_id.startswith(xlib.get_rnaquast_code()+'-'):
bioinfo_app_name = xlib.get_rnaquast_name()
elif result_dataset_id.startswith(xlib.get_rsem_code()+'-'):
bioinfo_app_name = xlib.get_rsem_name()
elif result_dataset_id.startswith(xlib.get_rsem_eval_code()+'-'):
bioinfo_app_name = xlib.get_rsem_eval_name()
elif result_dataset_id.startswith(xlib.get_samtools_code()+'-'):
bioinfo_app_name = xlib.get_samtools_name()
elif result_dataset_id.startswith(xlib.get_soapdenovotrans_code()+'-'):
bioinfo_app_name = xlib.get_soapdenovotrans_name()
elif result_dataset_id.startswith(xlib.get_star_code()+'-'):
bioinfo_app_name = xlib.get_star_name()
elif result_dataset_id.startswith(xlib.get_transabyss_code()+'-'):
bioinfo_app_name = xlib.get_transabyss_name()
elif result_dataset_id.startswith(xlib.get_transcript_filter_code()+'-'):
bioinfo_app_name = xlib.get_transcript_filter_name()
elif result_dataset_id.startswith(xlib.get_transcriptome_blastx_code()+'-'):
bioinfo_app_name = xlib.get_transcriptome_blastx_name()
elif result_dataset_id.startswith(xlib.get_transrate_code()+'-'):
bioinfo_app_name = xlib.get_transrate_name()
elif result_dataset_id.startswith(xlib.get_trimmomatic_code()+'-'):
bioinfo_app_name = xlib.get_trimmomatic_name()
elif result_dataset_id.startswith(xlib.get_trinity_code()+'-'):
bioinfo_app_name = xlib.get_trinity_name()
else:
bioinfo_app_name = 'xxx'
result_dataset_dict[result_dataset_id] = {'experiment_id': self.wrapper_experiment_id.get(), 'result_dataset_id': result_dataset_id, 'bioinfo_app': bioinfo_app_name, 'date': date, 'time': time}
# verify if there are any nodes running
if OK:
if result_dataset_dict == {}:
message = 'There is not any run.'
tkinter.messagebox.showwarning('{0} - {1}'.format(xlib.get_project_name(), self.head), message)
# build the data list
if OK:
data_list = ['experiment_id', 'result_dataset_id', 'bioinfo_app', 'date', 'time']
# build the data dictionary
if OK:
data_dict = {}
data_dict['experiment_id']= {'text': 'Experiment id. / Process', 'width': 200, 'aligment': 'left'}
data_dict['result_dataset_id'] = {'text': 'Result dataset', 'width': 200, 'aligment': 'left'}
data_dict['bioinfo_app'] = {'text': 'Bioinfo app / Utility', 'width': 200, 'aligment': 'left'}
data_dict['date'] = {'text': 'Date', 'width': 80, 'aligment': 'right'}
data_dict['time'] = {'text': 'Time', 'width': 80, 'aligment': 'right'}
# create the dialog Table to show the nodes running
if OK:
dialog_table = gdialogs.DialogTable(self, 'Experiment runs in {0}/{1}'.format(xlib.get_cluster_result_dir(), self.wrapper_experiment_id.get()), 400, 900, data_list, data_dict, result_dataset_dict, 'view_result_logs', [self.wrapper_cluster_name.get()])
self.wait_window(dialog_table)
# close the form
if OK:
self.close()
def create_gmap_config_file(experiment_id='exp001', reference_dataset_id='NONE', reference_file='NONE', assembly_dataset_id='sdnt-170101-235959', assembly_type='CONTIGS'):
'''
Create GMAP config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the app
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_star_code()):
assembly_software = xlib.get_star_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the GMAP config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_gmap_config_file())):
os.makedirs(os.path.dirname(get_gmap_config_file()))
with open(get_gmap_config_file(), mode='w', encoding='utf8') as file_id:
file_id.write('{0}\n'.format('# You must review the information of this file and update the values with the corresponding ones to the current run.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# The reference file must be located in the cluster directory {0}/experiment_id/reference_dataset_id'.format(xlib.get_cluster_reference_dir())))
file_id.write('{0}\n'.format('# The assembly files must be located in the cluster directory {0}/experiment_id/assembly_dataset_id'.format(xlib.get_cluster_result_dir())))
file_id.write('{0}\n'.format('# The experiment_id, reference_dataset_id, reference_file and assembly_dataset_id are fixed in the identification section.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# You can consult the parameters of GMAP and their meaning in http://research-pub.gene.com/gmap/.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# In section "GMAP parameters", the key "other_parameters" allows you to input additional parameters in the format:'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# other_parameters = --parameter-1[=value-1][; --parameter-2[=value-2][; ...; --parameter-n[=value-n]]]'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# parameter-i is a parameter name of GMAP and value-i a valid value of parameter-i, e.g.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# other_parameters = --no-chimeras; --canonical-mode=2'))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information identifies the experiment.'))
file_id.write('{0}\n'.format('[identification]'))
file_id.write('{0:<50} {1}\n'.format('experiment_id = {0}'.format(experiment_id), '# experiment identification'))
file_id.write('{0:<50} {1}\n'.format('reference_dataset_id = {0}'.format(reference_dataset_id), '# reference dataset identification or NONE'))
file_id.write('{0:<50} {1}\n'.format('reference_file = {0}'.format(reference_file), '# reference file name or NONE'))
file_id.write('{0:<50} {1}\n'.format('assembly_software = {0}'.format(assembly_software), '# assembly software: {0} ({1}) or {2} ({3}) or {4} ({5}) or {6} ({7}) or {8} ({9}) or {10} ({11})'.format(xlib.get_soapdenovotrans_code(), xlib.get_soapdenovotrans_name(), xlib.get_transabyss_code(), xlib.get_transabyss_name(), xlib.get_trinity_code(), xlib.get_trinity_name(), xlib.get_star_code(), xlib.get_star_name(), xlib.get_cd_hit_est_code(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code(), xlib.get_transcript_filter_name())))
file_id.write('{0:<50} {1}\n'.format('assembly_dataset_id = {0}'.format(assembly_dataset_id), '# assembly dataset identification'))
file_id.write('{0:<50} {1}\n'.format('assembly_type = {0}'.format(assembly_type), '# CONTIGS or SCAFFOLDS in {0}; NONE in {1}, {2}, {3}, {4} and {5}'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name())))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information to set the GMAP parameters'))
file_id.write('{0}\n'.format('[GMAP parameters]'))
file_id.write('{0:<50} {1}\n'.format('threads = 2', '# number of threads for use'))
file_id.write('{0:<50} {1}\n'.format('kmer = NONE', '# kmer size to use in genome database or NONE (the program will find the highest available kmer size in the genome database)'))
file_id.write('{0:<50} {1}\n'.format('sampling = NONE', '# Sampling to use in genome database or NONE (the program will find the smallest available sampling value in the genome database within selected k-mer size)'))
file_id.write('{0:<50} {1}\n'.format('input-buffer-size = 1000', '# size of input buffer'))
file_id.write('{0:<50} {1}\n'.format('output-buffer-size = 1000', '# size of buffer size in queries for output thread'))
file_id.write('{0:<50} {1}\n'.format('prunelevel = 0', '# pruning level: 0 (no pruning) or 1 (poor seqs) or 2 (repetitive seqs) or 3 (poor and repetitive)'))
file_id.write('{0:<50} {1}\n'.format('format = COMPRESS', '# format for output: COMPRESS or SUMMARY or ALIGN or PLS or GFF3_GENE or SPLICESITES or INTRONS or MAP_EXONS or MAP_RANGES or COORDS'))
file_id.write('{0:<50} {1}\n'.format('other_parameters = NONE', '# additional parameters to the previous ones or NONE'))
except:
error_list.append('*** ERROR: The file {0} can not be recreated'.format(get_gmap_config_file()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def build_busco_process_script(cluster_name, current_run_dir):
'''
Build the current BUSCO process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the BUSCO option dictionary
busco_option_dict = xlib.get_option_dict(get_busco_config_file())
# get the options
experiment_id = busco_option_dict['identification']['experiment_id']
assembly_software = busco_option_dict['identification'][
'assembly_software']
assembly_dataset_id = busco_option_dict['identification'][
'assembly_dataset_id']
assembly_type = busco_option_dict['identification']['assembly_type']
ncpu = busco_option_dict['BUSCO parameters']['ncpu']
lineage_data_url = busco_option_dict['BUSCO parameters'][
'lineage_data_url']
mode = busco_option_dict['BUSCO parameters']['mode'].lower()
evalue = busco_option_dict['BUSCO parameters']['evalue']
limit = busco_option_dict['BUSCO parameters']['limit']
species = busco_option_dict['BUSCO parameters']['species']
long = busco_option_dict['BUSCO parameters']['long'].upper()
augustus_options = busco_option_dict['BUSCO parameters'][
'augustus_options'].upper()
# get the file and name from the lineage data url
lineage_data_file = lineage_data_url.split("/")[-1]
# -- lineage_data = lineage_data_file[:lineage_data_file.find('.tar.gz')]
point_pos = lineage_data_file.find('.')
lineage_data = lineage_data_file[:point_pos]
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type == 'CONTIGS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.contig'
elif assembly_type == 'SCAFFOLDS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.scafSeq'
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/transabyss-final.fa'
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity.fasta'
elif assembly_software == xlib.get_ggtrinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity-GG.fasta'
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/clustered-transcriptome.fasta'
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/filtered-transcriptome.fasta'
# write the BUSCO process script
try:
if not os.path.exists(os.path.dirname(get_busco_process_script())):
os.makedirs(os.path.dirname(get_busco_process_script()))
with open(get_busco_process_script(),
mode='w',
encoding='iso-8859-1',
newline='\n') as script_file_id:
script_file_id.write('#!/bin/bash\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
'SEP="#########################################"\n')
script_file_id.write(
'export HOST_IP=`curl --silent checkip.amazonaws.com`\n')
script_file_id.write(
'export HOST_ADDRESS="ec2-${HOST_IP//./-}-compute-1.amazonaws.com"\n'
)
script_file_id.write(
'export AWS_CONFIG_FILE=/home/ubuntu/.aws/config\n')
script_file_id.write(
'export AWS_SHARED_CREDENTIALS_FILE=/home/ubuntu/.aws/credentials\n'
)
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
f'MINICONDA3_BIN_PATH={xlib.get_cluster_app_dir()}/{xlib.get_miniconda3_name()}/bin\n'
)
script_file_id.write(f'export PATH=$MINICONDA3_BIN_PATH:$PATH\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
f'STATUS_DIR={xlib.get_status_dir(current_run_dir)}\n')
script_file_id.write(
f'SCRIPT_STATUS_OK={xlib.get_status_ok(current_run_dir)}\n')
script_file_id.write(
f'SCRIPT_STATUS_WRONG={xlib.get_status_wrong(current_run_dir)}\n'
)
script_file_id.write('mkdir --parents $STATUS_DIR\n')
script_file_id.write(
'if [ -f $SCRIPT_STATUS_OK ]; then rm $SCRIPT_STATUS_OK; fi\n')
script_file_id.write(
'if [ -f $SCRIPT_STATUS_WRONG ]; then rm $SCRIPT_STATUS_WRONG; fi\n'
)
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(f'CURRENT_DIR={current_run_dir}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function init\n')
script_file_id.write('{\n')
script_file_id.write(' INIT_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(
' echo "Script started at $FORMATTED_INIT_DATETIME+00:00."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(f' echo "CLUSTER: {cluster_name}"\n')
script_file_id.write(' echo "HOST NAME: $HOSTNAME"\n')
script_file_id.write(' echo "HOST IP: $HOST_IP"\n')
script_file_id.write(' echo "HOST ADDRESS: $HOST_ADDRESS"\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function download_lineage_data\n')
script_file_id.write('{\n')
script_file_id.write(' cd $CURRENT_DIR\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' echo "Downloading lineage data ..."\n')
download_script = f'import requests; r = requests.get(\'{lineage_data_url}\') ; open(\'{lineage_data_file}\' , \'wb\').write(r.content)'
script_file_id.write(
f' $MINICONDA3_BIN_PATH/python3 -c "{download_script}"\n')
script_file_id.write(' RC=$?\n')
script_file_id.write(
' if [ $RC -ne 0 ]; then manage_error download_script $RC; fi\n'
)
script_file_id.write(f' tar -xzvf ./{lineage_data_file}\n')
script_file_id.write(' RC=$?\n')
script_file_id.write(
' if [ $RC -ne 0 ]; then manage_error tar $RC; fi\n')
script_file_id.write(f' rm ./{lineage_data_file}\n')
script_file_id.write(' RC=$?\n')
script_file_id.write(
' if [ $RC -ne 0 ]; then manage_error rm $RC; fi\n')
script_file_id.write(' echo "Lineage data are downloaded."\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function run_busco_process\n')
script_file_id.write('{\n')
script_file_id.write(
f' source activate {xlib.get_busco_anaconda_code()}\n')
script_file_id.write(' cd $CURRENT_DIR\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(
' echo "Assessing the transcriptome quality ..."\n')
script_file_id.write(' /usr/bin/time \\\n')
script_file_id.write(
f' --format="{xlib.get_time_output_format(separator=False)}" \\\n'
)
script_file_id.write(' busco \\\n')
script_file_id.write(f' --cpu={ncpu} \\\n')
script_file_id.write(
f' --lineage_dataset=./{lineage_data} \\\n')
script_file_id.write(f' --mode={mode} \\\n')
script_file_id.write(f' --evalue={evalue} \\\n')
script_file_id.write(f' --limit={limit} \\\n')
if species.upper() != 'NONE':
script_file_id.write(f' --species={species} \\\n')
if long == 'YES':
script_file_id.write(' --long \\\n')
if augustus_options.upper() != 'NONE':
script_file_id.write(
f' --august_options="{augustus_options}" \\\n')
script_file_id.write(f' --in={transcriptome_file} \\\n')
script_file_id.write(
f' --out={os.path.basename(current_run_dir)}\n')
script_file_id.write(' RC=$?\n')
script_file_id.write(
' if [ $RC -ne 0 ]; then manage_error run_BUSCO.py $RC; fi\n'
)
script_file_id.write(' echo "The assessment is done."\n')
script_file_id.write(' conda deactivate\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function end\n')
script_file_id.write('{\n')
script_file_id.write(' END_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' calculate_duration\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(
' echo "Script ended OK at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' send_mail ok\n')
script_file_id.write(' touch $SCRIPT_STATUS_OK\n')
script_file_id.write(' exit 0\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function manage_error\n')
script_file_id.write('{\n')
script_file_id.write(' END_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' calculate_duration\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' echo "ERROR: $1 returned error $2"\n')
script_file_id.write(
' echo "Script ended WRONG at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' send_mail wrong\n')
script_file_id.write(' touch $SCRIPT_STATUS_WRONG\n')
script_file_id.write(' exit 3\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
process_name = f'{xlib.get_busco_name()} process'
mail_message_ok = xlib.get_mail_message_ok(process_name,
cluster_name)
mail_message_wrong = xlib.get_mail_message_wrong(
process_name, cluster_name)
script_file_id.write('function send_mail\n')
script_file_id.write('{\n')
script_file_id.write(
f' SUBJECT="{xlib.get_project_name()}: {process_name}"\n')
script_file_id.write(' if [ "$1" == "ok" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_ok}"\n')
script_file_id.write(' elif [ "$1" == "wrong" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_wrong}"\n')
script_file_id.write(' else\n')
script_file_id.write(' MESSAGE=""\n')
script_file_id.write(' fi\n')
script_file_id.write(
' DESTINATION_FILE=mail-destination.json\n')
script_file_id.write(' echo "{" > $DESTINATION_FILE\n')
script_file_id.write(
f' echo " \\\"ToAddresses\\\": [\\\"{xconfiguration.get_contact_data()}\\\"]," >> $DESTINATION_FILE\n'
)
script_file_id.write(
' echo " \\\"CcAddresses\\\": []," >> $DESTINATION_FILE\n'
)
script_file_id.write(
' echo " \\\"BccAddresses\\\": []" >> $DESTINATION_FILE\n'
)
script_file_id.write(' echo "}" >> $DESTINATION_FILE\n')
script_file_id.write(' MESSAGE_FILE=mail-message.json\n')
script_file_id.write(' echo "{" > $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Subject\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Data\\\": \\\"$SUBJECT\\\"," >> $MESSAGE_FILE\n'
)
script_file_id.write(
' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n'
)
script_file_id.write(' echo " }," >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Body\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Html\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Data\\\": \\\"$MESSAGE\\\"," >> $MESSAGE_FILE\n'
)
script_file_id.write(
' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n'
)
script_file_id.write(' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write(' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write(' echo "}" >> $MESSAGE_FILE\n')
script_file_id.write(
f' aws ses send-email --from {xconfiguration.get_contact_data()} --destination file://$DESTINATION_FILE --message file://$MESSAGE_FILE\n'
)
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function calculate_duration\n')
script_file_id.write('{\n')
script_file_id.write(
' DURATION=`expr $END_DATETIME - $INIT_DATETIME`\n')
script_file_id.write(' HH=`expr $DURATION / 3600`\n')
script_file_id.write(' MM=`expr $DURATION % 3600 / 60`\n')
script_file_id.write(' SS=`expr $DURATION % 60`\n')
script_file_id.write(
' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`\n'
)
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('init\n')
script_file_id.write('download_lineage_data\n')
script_file_id.write('run_busco_process\n')
script_file_id.write('end\n')
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append(
f'*** ERROR: The file {get_busco_process_script()} can not be created'
)
OK = False
# return the control variable and the error list
return (OK, error_list)
def validate_cd_hit_est_config_file(strict):
'''
Validate the CD-HIT-EST config file of a run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# intitialize variable used when value is not found
not_found = '***NOTFOUND***'.upper()
# get the option dictionary
try:
cd_hit_est_option_dict = xlib.get_option_dict(
get_cd_hit_est_config_file())
except:
error_list.append('*** ERROR: The syntax is WRONG.')
OK = False
else:
# get the sections list
sections_list = []
for section in cd_hit_est_option_dict.keys():
sections_list.append(section)
sections_list.sort()
# check section "identification"
if 'identification' not in sections_list:
error_list.append(
'*** ERROR: the section "identification" is not found.')
OK = False
else:
# check section "identification" - key "experiment_id"
experiment_id = cd_hit_est_option_dict.get(
'identification', {}).get('experiment_id', not_found)
if experiment_id == not_found:
error_list.append(
'*** ERROR: the key "experiment_id" is not found in the section "identification".'
)
OK = False
# check section "identification" - key "assembly_software"
assembly_software = cd_hit_est_option_dict.get(
'identification', {}).get('assembly_software', not_found)
if assembly_software == not_found:
error_list.append(
'*** ERROR: the key "assembly_software" is not found in the section "identification".'
)
OK = False
elif assembly_software not in [
xlib.get_soapdenovotrans_code(),
xlib.get_transabyss_code(),
xlib.get_trinity_code(),
xlib.get_star_code(),
xlib.get_cd_hit_est_code(),
xlib.get_transcript_filter_code()
]:
error_list.append(
'*** ERROR: the key "assembly_software" value in the section "identification" must be {0} or {1} or {2} or {3} or {4} OR {5}.'
.format(xlib.get_soapdenovotrans_code(),
xlib.get_transabyss_code(),
xlib.get_trinity_code(), xlib.get_star_code(),
xlib.get_cd_hit_est_code(),
xlib.get_transcript_filter_code()))
OK = False
# check section "identification" - key "assembly_dataset_id"
assembly_dataset_id = cd_hit_est_option_dict.get(
'identification', {}).get('assembly_dataset_id', not_found)
if assembly_dataset_id == not_found:
error_list.append(
'*** ERROR: the key "assembly_dataset_id" is not found in the section "identification".'
)
OK = False
elif not assembly_dataset_id.startswith(
xlib.get_soapdenovotrans_code()
) and not assembly_dataset_id.startswith(xlib.get_transabyss_code(
)) and not assembly_dataset_id.startswith(xlib.get_trinity_code(
)) and not assembly_dataset_id.startswith(xlib.get_star_code(
)) and not assembly_dataset_id.startswith(xlib.get_cd_hit_est_code(
)) and not assembly_dataset_id.startswith(
xlib.get_transcript_filter_code()):
error_list.append(
'*** ERROR: the key "assembly_dataset_id" value is not a {0} nor {1} nor {2} nor {3} nor {4} nor {5} assembly.'
.format(xlib.get_soapdenovotrans_name(),
xlib.get_transabyss_name(),
xlib.get_trinity_name(), xlib.get_star_name(),
xlib.get_cd_hit_est_name(),
xlib.get_transcript_filter_code()))
OK = False
# check section "identification" - key "assembly_type"
assembly_type = cd_hit_est_option_dict.get(
'identification', {}).get('assembly_type', not_found)
if assembly_type == not_found:
error_list.append(
'*** ERROR: the key "assembly_type" is not found in the section "identification".'
)
OK = False
elif assembly_dataset_id.startswith(
xlib.get_soapdenovotrans_code()):
if assembly_type.upper() not in ['CONTIGS', 'SCAFFOLDS']:
error_list.append(
'*** ERROR: the key "assembly_type" must be "CONTIGS" or "SCAFFOLDS" when {0} is the assembly software.'
.format(xlib.get_soapdenovotrans_name()))
OK = False
elif assembly_dataset_id.startswith(xlib.get_transabyss_code(
)) or assembly_dataset_id.startswith(xlib.get_trinity_code(
)) or assembly_dataset_id.startswith(
xlib.get_star_code()) or assembly_dataset_id.startswith(
xlib.get_cd_hit_est_code(
)) or assembly_dataset_id.startswith(
xlib.get_transcript_filter_code()):
if assembly_type.upper() != 'NONE':
error_list.append(
'*** ERROR: the key "assembly_type" must be "NONE" when {0} or {1} or {2} or {3} or {4} is the assembly software.'
.format(xlib.get_transabyss_name(),
xlib.get_trinity_name(), xlib.get_star_name(),
xlib.get_cd_hit_est_name(),
xlib.get_transcript_filter_name()))
OK = False
# check section "CD-HIT-EST parameters"
if 'CD-HIT-EST parameters' not in sections_list:
error_list.append(
'*** ERROR: the section "CD-HIT-EST parameters" is not found.')
OK = False
else:
# check section "CD-HIT-EST parameters" - key "threads"
threads = cd_hit_est_option_dict.get('CD-HIT-EST parameters',
{}).get('threads', not_found)
if threads == not_found:
error_list.append(
'*** ERROR: the key "threads" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
if int(threads) < 0:
error_list.append(
'*** ERROR: the key "threads" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 0.'
)
OK = False
except:
error_list.append(
'*** ERROR: the key "threads" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 0.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "memory_limit"
memory_limit = cd_hit_est_option_dict.get(
'CD-HIT-EST parameters', {}).get('memory_limit', not_found)
if memory_limit == not_found:
error_list.append(
'*** ERROR: the key "memory_limit" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
if int(memory_limit) < 0:
error_list.append(
'*** ERROR: the key "memory_limit" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 0.'
)
OK = False
except:
error_list.append(
'*** ERROR: the key "memory_limit" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 0.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "seq_identity_threshold"
seq_identity_threshold = cd_hit_est_option_dict.get(
'CD-HIT-EST parameters', {}).get('seq_identity_threshold',
not_found)
if seq_identity_threshold == not_found:
error_list.append(
'*** ERROR: the key "seq_identity_threshold" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
if float(seq_identity_threshold) < 0.0 or float(
seq_identity_threshold) > 1.0:
error_list.append(
'*** ERROR: the key "seq_identity_threshold" in the section "CD-HIT-EST parameters" must be a float value between 0.0 and 1.0.'
)
OK = False
except:
error_list.append(
'*** ERROR: the key "seq_identity_threshold" in the section "CD-HIT-EST parameters" must be a float value between 0.0 and 1.0.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "word_length"
word_length = cd_hit_est_option_dict.get(
'CD-HIT-EST parameters', {}).get('word_length', not_found)
if word_length == not_found:
error_list.append(
'*** ERROR: the key "word_length" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
if int(word_length) < 1:
error_list.append(
'*** ERROR: the key "word_length" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 1.'
)
OK = False
except:
error_list.append(
'*** ERROR: the key "word_length" in the section "CD-HIT-EST parameters" must be an integer value greater or equal to 1.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "mask"
mask = cd_hit_est_option_dict.get('CD-HIT-EST parameters',
{}).get('mask',
not_found).upper()
if mask == not_found:
error_list.append(
'*** ERROR: the key "mask" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
# check section "CD-HIT-EST parameters" - key "match"
match = cd_hit_est_option_dict.get('CD-HIT-EST parameters',
{}).get('match', not_found)
if match == not_found:
error_list.append(
'*** ERROR: the key "match" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
int(match)
except:
error_list.append(
'*** ERROR: the key "match" in the section "CD-HIT-EST parameters" must be an integer value.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "mismatch"
mismatch = cd_hit_est_option_dict.get('CD-HIT-EST parameters',
{}).get(
'mismatch', not_found)
if mismatch == not_found:
error_list.append(
'*** ERROR: the key "mismatch" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
try:
int(mismatch)
except:
error_list.append(
'*** ERROR: the key "match" in the section "CD-HIT-EST parameters" must be an integer value.'
)
OK = False
# check section "CD-HIT-EST parameters" - key "other_parameters"
not_allowed_parameters_list = [
'T', 'M', 'c', 'n', 'mask', 'match', 'mismatch'
]
other_parameters = cd_hit_est_option_dict.get(
'CD-HIT-EST parameters', {}).get('other_parameters', not_found)
if other_parameters == not_found:
error_list.append(
'*** ERROR: the key "other_parameters" is not found in the section "CD-HIT-EST parameters".'
)
OK = False
else:
if other_parameters.upper() != 'NONE':
parameter_list = [
x.strip() for x in other_parameters.split(';')
]
for parameter in parameter_list:
try:
if parameter.find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
except:
error_list.append(
'*** ERROR: the value of the key "other_parameters" in the section "CD-HIT-EST parameters" must be NONE or a valid parameter list.'
)
OK = False
break
if parameter_name in not_allowed_parameters_list:
error_list.append(
'*** ERROR: the parameter {0} is not allowed in the key "other_parameters" of the section "CD-HIT-EST parameters" because it is controled by {1}.'
.format(parameter_name,
xlib.get_project_name()))
OK = False
# warn that the results config file is not valid if there are any errors
if not OK:
error_list.append(
'\nThe {0} config file is not valid. Please, correct this file or recreate it.'
.format(xlib.get_cd_hit_est_name()))
# return the control variable and the error list
return (OK, error_list)
def build_quast_process_script(cluster_name, current_run_dir):
'''
Build the current QUAST process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the QUAST option dictionary
quast_option_dict = xlib.get_option_dict(get_quast_config_file())
# get the options
experiment_id = quast_option_dict['identification']['experiment_id']
reference_dataset_id = quast_option_dict['identification']['reference_dataset_id']
reference_file = quast_option_dict['identification']['reference_file']
assembly_software = quast_option_dict['identification']['assembly_software']
assembly_dataset_id = quast_option_dict['identification']['assembly_dataset_id']
assembly_type = quast_option_dict['identification']['assembly_type']
threads = quast_option_dict['QUAST parameters']['threads']
# set the reference file path
if reference_dataset_id.upper() != 'NONE':
reference_file_path = xlib.get_cluster_reference_file(reference_dataset_id, reference_file)
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type.upper() == 'CONTIGS':
transcriptome_file = '{0}/{1}-{2}.contig'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_type.upper() == 'SCAFFOLDS':
transcriptome_file = '{0}/{1}-{2}.scafSeq'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = '{0}/transabyss-final.fa'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = '{0}/Trinity.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_star_code():
transcriptome_file = '{0}/Trinity-GG.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = '{0}/clustered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = '{0}/filtered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
# get the QUAST process script name
quast_process_script = get_quast_process_script()
# write the QUAST process script
try:
if not os.path.exists(os.path.dirname(quast_process_script)):
os.makedirs(os.path.dirname(quast_process_script))
with open(quast_process_script, mode='w', encoding='utf8', newline='\n') as file_id:
file_id.write('{0}\n'.format('#!/bin/bash'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('QUAST_PATH={0}/{1}/envs/{2}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name(), xlib.get_quast_bioconda_code())))
file_id.write('{0}\n'.format('PATH=$QUAST_PATH:$PATH'))
file_id.write('{0}\n'.format('SEP="#########################################"'))
file_id.write('{0}\n'.format('cd {0}/{1}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name())))
file_id.write('{0}\n'.format('source activate {0}'.format(xlib.get_quast_bioconda_code())))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function init'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' INIT_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script started in node $HOSTNAME of cluster {0} at $FORMATTED_INIT_DATETIME UTC."'.format(cluster_name)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function run_quast_process'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' quast.py --version'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' /usr/bin/time \\'))
file_id.write('{0}\n'.format(' --format="$SEP\\nElapsed real time (s): %e\\nCPU time in kernel mode (s): %S\\nCPU time in user mode (s): %U\\nPercentage of CPU: %P\\nMaximum resident set size(Kb): %M\\nAverage total memory use (Kb):%K" \\'))
file_id.write('{0}\n'.format(' quast.py \\'))
file_id.write('{0}\n'.format(' --threads {0} \\'.format(threads)))
file_id.write('{0}\n'.format(' --output-dir {0} \\'.format(current_run_dir)))
if reference_dataset_id.upper() != 'NONE':
file_id.write('{0}\n'.format(' -R {0} \\'.format(reference_file_path)))
if assembly_type.upper() == 'SCAFFOLDS':
file_id.write('{0}\n'.format(' --scaffolds \\'))
file_id.write('{0}\n'.format(' {0}'.format(transcriptome_file)))
file_id.write('{0}\n'.format(' RC=$?'))
file_id.write('{0}\n'.format(' if [ $RC -ne 0 ]; then manage_error quast.py $RC; fi'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function end'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script ended OK at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_quast_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended OK at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_quast_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 0'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function manage_error'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "ERROR: $1 returned error $2"'))
file_id.write('{0}\n'.format(' echo "Script ended WRONG at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_quast_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended WRONG at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_quast_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 3'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function calculate_duration'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' DURATION=`expr $END_DATETIME - $INIT_DATETIME`'))
file_id.write('{0}\n'.format(' HH=`expr $DURATION / 3600`'))
file_id.write('{0}\n'.format(' MM=`expr $DURATION % 3600 / 60`'))
file_id.write('{0}\n'.format(' SS=`expr $DURATION % 60`'))
file_id.write('{0}\n'.format(' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('init'))
file_id.write('{0}\n'.format('run_quast_process'))
file_id.write('{0}\n'.format('end'))
except:
error_list.append('*** ERROR: The file {0} can not be created'.format(quast_process_script))
OK = False
# return the control variable and the error list
return (OK, error_list)
def validate_quast_config_file(strict):
'''
Validate the QUAST config file of a run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# intitialize variable used when value is not found
not_found = '***NOTFOUND***'.upper()
# get the option dictionary
try:
quast_option_dict = xlib.get_option_dict(get_quast_config_file())
except:
error_list.append('*** ERROR: The syntax is WRONG.')
OK = False
else:
# get the sections list
sections_list = []
for section in quast_option_dict.keys():
sections_list.append(section)
sections_list.sort()
# check section "identification"
if 'identification' not in sections_list:
error_list.append('*** ERROR: the section "identification" is not found.')
OK = False
else:
# check section "identification" - key "experiment_id"
experiment_id = quast_option_dict.get('identification', {}).get('experiment_id', not_found)
if experiment_id == not_found:
error_list.append('*** ERROR: the key "experiment_id" is not found in the section "identification".')
OK = False
# check section "identification" - key "reference_dataset_id"
reference_dataset_id = quast_option_dict.get('identification', {}).get('reference_dataset_id', not_found)
if reference_dataset_id == not_found:
error_list.append('*** ERROR: the key "reference_dataset_id" is not found in the section "identification".')
OK = False
# check section "identification" - key "reference_file"
reference_file = quast_option_dict.get('identification', {}).get('reference_file', not_found)
if reference_file == not_found:
error_list.append('*** ERROR: the key "reference_file" is not found in the section "identification".')
OK = False
# check section "identification" - key "assembly_software"
assembly_software = quast_option_dict.get('identification', {}).get('assembly_software', not_found)
if assembly_software == not_found:
error_list.append('*** ERROR: the key "assembly_software" is not found in the section "identification".')
OK = False
elif assembly_software not in [xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()]:
error_list.append('*** ERROR: the key "assembly_software" value in the section "identification" must be {0} or {1} or {2} or {3} or {4} OR {5}.'.format(xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()))
OK = False
# check section "identification" - key "assembly_dataset_id"
assembly_dataset_id = quast_option_dict.get('identification', {}).get('assembly_dataset_id', not_found)
if assembly_dataset_id == not_found:
error_list.append('*** ERROR: the key "assembly_dataset_id" is not found in the section "identification".')
OK = False
elif not assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()) and not assembly_dataset_id.startswith(xlib.get_transabyss_code()) and not assembly_dataset_id.startswith(xlib.get_trinity_code()) and not assembly_dataset_id.startswith(xlib.get_star_code()) and not assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) and not assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
error_list.append('*** ERROR: the key "assembly_dataset_id" value is not a {0} nor {1} nor {2} nor {3} nor {4} nor {5} assembly.'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code()))
OK = False
# check section "identification" - key "assembly_type"
assembly_type = quast_option_dict.get('identification', {}).get('assembly_type', not_found)
if assembly_type == not_found:
error_list.append('*** ERROR: the key "assembly_type" is not found in the section "identification".')
OK = False
elif assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
if assembly_type.upper() not in ['CONTIGS', 'SCAFFOLDS']:
error_list.append('*** ERROR: the key "assembly_type" must be "CONTIGS" or "SCAFFOLDS" when {0} is the assembly software.'.format(xlib.get_soapdenovotrans_name()))
OK = False
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()) or assembly_dataset_id.startswith(xlib.get_trinity_code()) or assembly_dataset_id.startswith(xlib.get_star_code()) or assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) or assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
if assembly_type.upper() != 'NONE':
error_list.append('*** ERROR: the key "assembly_type" must be "NONE" when {0} or {1} or {2} or {3} or {4} is the assembly software.'.format(xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name()))
OK = False
# check section "QUAST parameters"
if 'QUAST parameters' not in sections_list:
error_list.append('*** ERROR: the section "QUAST parameters" is not found.')
OK = False
else:
# check section "QUAST parameters" - key "threads"
threads = quast_option_dict.get('QUAST parameters', {}).get('threads', not_found)
if threads == not_found:
error_list.append('*** ERROR: the key "threads" is not found in the section "QUAST parameters".')
OK = False
else:
try:
if int(threads) < 1:
error_list.append('*** ERROR: the key "threads" in the section "QUAST parameters" must be an integer value greater or equal to 1.')
OK = False
except:
error_list.append('*** ERROR: the key "threads" in the section "QUAST parameters" must be an integer value greater or equal to 1.')
OK = False
# warn that the results config file is not valid if there are any errors
if not OK:
error_list.append('\nThe {0} config file is not valid. Please, correct this file or recreate it.'.format(xlib.get_quast_name()))
# return the control variable and the error list
return (OK, error_list)
def build_busco_process_script(cluster_name, current_run_dir):
'''
Build the current BUSCO process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the BUSCO option dictionary
busco_option_dict = xlib.get_option_dict(get_busco_config_file())
# get the options
experiment_id = busco_option_dict['identification']['experiment_id']
assembly_software = busco_option_dict['identification']['assembly_software']
assembly_dataset_id = busco_option_dict['identification']['assembly_dataset_id']
assembly_type = busco_option_dict['identification']['assembly_type']
ncpu = busco_option_dict['BUSCO parameters']['ncpu']
lineage_data = busco_option_dict['BUSCO parameters']['lineage_data']
lineage_data_file = '{0}.tar.gz'.format(lineage_data)
lineage_data_url = 'http://busco.ezlab.org/v2/datasets/{0}'.format(lineage_data_file)
mode = busco_option_dict['BUSCO parameters']['mode'].lower()
evalue = busco_option_dict['BUSCO parameters']['evalue']
limit = busco_option_dict['BUSCO parameters']['limit']
species = busco_option_dict['BUSCO parameters']['species']
long = busco_option_dict['BUSCO parameters']['long'].upper()
augustus_options = busco_option_dict['BUSCO parameters']['augustus_options'].upper()
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type == 'CONTIGS':
transcriptome_file = '{0}/{1}-{2}.contig'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_type == 'SCAFFOLDS':
transcriptome_file = '{0}/{1}-{2}.scafSeq'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = '{0}/transabyss-final.fa'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = '{0}/Trinity.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_star_code():
transcriptome_file = '{0}/Trinity-GG.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = '{0}/clustered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = '{0}/filtered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
# write the BUSCO process script
try:
if not os.path.exists(os.path.dirname(get_busco_process_script())):
os.makedirs(os.path.dirname(get_busco_process_script()))
with open(get_busco_process_script(), mode='w', encoding='utf8', newline='\n') as file_id:
file_id.write('{0}\n'.format('#!/bin/bash'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('BUSCO_PATH={0}/{1}/envs/{2}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name(), xlib.get_busco_bioconda_code())))
file_id.write('{0}\n'.format('export PATH=$BUSCO_PATH:$PATH'))
file_id.write('{0}\n'.format('SEP="#########################################"'))
file_id.write('{0}\n'.format('cd {0}/{1}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name())))
file_id.write('{0}\n'.format('source activate {0}'.format(xlib.get_busco_bioconda_code())))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function init'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' INIT_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script started in node $HOSTNAME of cluster {0} at $FORMATTED_INIT_DATETIME UTC."'.format(cluster_name)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function download_lineage_data'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Downloading lineage data ..."'))
file_id.write('{0}\n'.format(' wget --quiet --output-document ./{0} {1}'.format(lineage_data_file, lineage_data_url)))
file_id.write('{0}\n'.format(' tar -xzvf ./{0}'.format(lineage_data_file)))
file_id.write('{0}\n'.format(' rm ./{0}'.format(lineage_data_file)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function run_busco_process'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' run_BUSCO.py --version'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' /usr/bin/time \\'))
file_id.write('{0}\n'.format(' --format="$SEP\\nElapsed real time (s): %e\\nCPU time in kernel mode (s): %S\\nCPU time in user mode (s): %U\\nPercentage of CPU: %P\\nMaximum resident set size(Kb): %M\\nAverage total memory use (Kb):%K" \\'))
file_id.write('{0}\n'.format(' run_BUSCO.py \\'))
file_id.write('{0}\n'.format(' --cpu={0} \\'.format(ncpu)))
file_id.write('{0}\n'.format(' --lineage_path=./{0} \\'.format(lineage_data)))
file_id.write('{0}\n'.format(' --mode={0} \\'.format(mode)))
file_id.write('{0}\n'.format(' --evalue={0} \\'.format(evalue)))
file_id.write('{0}\n'.format(' --limit={0} \\'.format(limit)))
if species.upper() != 'NONE':
file_id.write('{0}\n'.format(' --species={0} \\'.format(species)))
if long == 'YES':
file_id.write('{0}\n'.format(' --long \\'))
if augustus_options.upper() != 'NONE':
file_id.write('{0}\n'.format(" --august_options='{0}' \\".format(augustus_options)))
file_id.write('{0}\n'.format(' --in={0} \\'.format(transcriptome_file)))
file_id.write('{0}\n'.format(' --out={0}'.format(os.path.basename(current_run_dir))))
file_id.write('{0}\n'.format(' RC=$?'))
file_id.write('{0}\n'.format(' if [ $RC -ne 0 ]; then manage_error run_BUSCO.py $RC; fi'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function end'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script ended OK at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_busco_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended OK at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_busco_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 0'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function manage_error'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "ERROR: $1 returned error $2"'))
file_id.write('{0}\n'.format(' echo "Script ended WRONG at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_busco_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended WRONG at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_busco_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 3'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function calculate_duration'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' DURATION=`expr $END_DATETIME - $INIT_DATETIME`'))
file_id.write('{0}\n'.format(' HH=`expr $DURATION / 3600`'))
file_id.write('{0}\n'.format(' MM=`expr $DURATION % 3600 / 60`'))
file_id.write('{0}\n'.format(' SS=`expr $DURATION % 60`'))
file_id.write('{0}\n'.format(' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('init'))
file_id.write('{0}\n'.format('download_lineage_data'))
file_id.write('{0}\n'.format('run_busco_process'))
file_id.write('{0}\n'.format('end'))
except:
error_list.append('*** ERROR: The file {0} can not be created'.format(get_busco_process_script()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def create_busco_config_file(experiment_id='exp001', assembly_dataset_id='sdnt-170101-235959', assembly_type='CONTIGS'):
'''
Create BUSCO config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the assembly software
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_star_code()):
assembly_software = xlib.get_star_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the BUSCO config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_busco_config_file())):
os.makedirs(os.path.dirname(get_busco_config_file()))
with open(get_busco_config_file(), mode='w', encoding='utf8') as file_id:
file_id.write('{0}\n'.format('# You must review the information of this file and update the values with the corresponding ones to the current run.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# The reference file must be located in the cluster directory {0}/experiment_id/reference_dataset_id'.format(xlib.get_cluster_reference_dir())))
file_id.write('{0}\n'.format('# The assembly files must be located in the cluster directory {0}/experiment_id/assembly_dataset_id'.format(xlib.get_cluster_result_dir())))
file_id.write('{0}\n'.format('# The experiment_id and assembly_dataset_id names are fixed in the identification section.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# In section "BUSCO parameters", the key "augustus_options" allows you to input additional August parameters in the format:'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# augustus_options = --parameter-1[=value-1][; --parameter-2[=value-2][; ...; --parameter-n[=value-n]]]'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# parameter-i is a parameter name of Augustus and value-i a valid value of parameter-i, e.g.'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# augustus_options = --translation_table=6 --progress=true)'))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format('# You can consult the parameters of BUSCO and their meaning in http://busco.ezlab.org/.'))
file_id.write('{0}\n'.format('# and August ones in http://bioinf.uni-greifswald.de/augustus/.'))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information identifies the experiment.'))
file_id.write('{0}\n'.format('[identification]'))
file_id.write('{0:<50} {1}\n'.format('experiment_id = {0}'.format(experiment_id), '# experiment identification'))
file_id.write('{0:<50} {1}\n'.format('assembly_software = {0}'.format(assembly_software), '# assembly software: {0} ({1}) or {2} ({3}) or {4} ({5}) or {6} ({7}) or {8} ({9}) or {10} ({11})'.format(xlib.get_soapdenovotrans_code(), xlib.get_soapdenovotrans_name(), xlib.get_transabyss_code(), xlib.get_transabyss_name(), xlib.get_trinity_code(), xlib.get_trinity_name(), xlib.get_star_code(), xlib.get_star_name(), xlib.get_cd_hit_est_code(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code(), xlib.get_transcript_filter_name())))
file_id.write('{0:<50} {1}\n'.format('assembly_dataset_id = {0}'.format(assembly_dataset_id), '# assembly dataset identification'))
file_id.write('{0:<50} {1}\n'.format('assembly_type = {0}'.format(assembly_type), '# CONTIGS or SCAFFOLDS in {0}; NONE in {1}, {2}, {3}, {4} and {5}'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name())))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format('# This section has the information to set the BUSCO parameters'))
file_id.write('{0}\n'.format('[BUSCO parameters]'))
file_id.write('{0:<50} {1}\n'.format('ncpu = 2', '# number of threads/cores for use'))
file_id.write('{0:<50} {1}\n'.format('lineage_data = embryophyta_odb9', '# value to find the lineage data url in BUSCO web (e.g. embryophyta -> http://busco.ezlab.org/v2/datasets/embryophyta_odb9.tar.gz)'))
file_id.write('{0:<50} {1}\n'.format('mode = tran', '# geno (genome assemblies, DNA) or tran (transcriptome assemblies, DNA) or prot (annotated gene sets, proteins)'))
file_id.write('{0:<50} {1}\n'.format('evalue = 1e-03', '# E-value cutoff for BLAST searches'))
file_id.write('{0:<50} {1}\n'.format('limit = 3', '# number of candidate regions to consider'))
file_id.write('{0:<50} {1}\n'.format('species = NONE', '# identifier of existing Augustus species gene finding parameters or NONE'))
file_id.write('{0:<50} {1}\n'.format('long = NO', '# Augustus optimization mode for self-training: YES or NO'))
file_id.write('{0:<50} {1}\n'.format('augustus_options = NONE', '# additional parameters to August or NONE'))
except:
error_list.append('*** ERROR: The file {0} can not be recreated'.format(get_busco_config_file()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def validate_busco_config_file(strict):
'''
Validate the BUSCO config file of a run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# intitialize variable used when value is not found
not_found = '***NOTFOUND***'.upper()
# get the option dictionary
try:
busco_option_dict = xlib.get_option_dict(get_busco_config_file())
except:
error_list.append('*** ERROR: The syntax is WRONG.')
OK = False
else:
# get the sections list
sections_list = []
for section in busco_option_dict.keys():
sections_list.append(section)
sections_list.sort()
# check section "identification"
if 'identification' not in sections_list:
error_list.append('*** ERROR: the section "identification" is not found.')
OK = False
else:
# check section "identification" - key "experiment_id"
experiment_id = busco_option_dict.get('identification', {}).get('experiment_id', not_found)
is_experiment_id_OK = True
if experiment_id == not_found:
error_list.append('*** ERROR: the key "experiment_id" is not found in the section "identification".')
is_experiment_id_OK = False
OK = False
# check section "identification" - key "assembly_software"
assembly_software = busco_option_dict.get('identification', {}).get('assembly_software', not_found)
is_assembly_software_OK = True
if assembly_software == not_found:
error_list.append('*** ERROR: the key "assembly_software" is not found in the section "identification".')
is_assembly_software_OK = False
OK = False
elif assembly_software not in [xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()]:
error_list.append('*** ERROR: the key "assembly_software" value in the section "identification" must be {0} or {1} or {2} or {3} or {4} OR {5}.'.format(xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()))
is_assembly_software_OK = False
OK = False
# check section "identification" - key "assembly_dataset_id"
assembly_dataset_id = busco_option_dict.get('identification', {}).get('assembly_dataset_id', not_found)
is_assembly_dataset_id_OK = True
if assembly_dataset_id == not_found:
error_list.append('*** ERROR: the key "assembly_dataset_id" is not found in the section "identification".')
is_assembly_dataset_id_OK = False
OK = False
elif not assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()) and not assembly_dataset_id.startswith(xlib.get_transabyss_code()) and not assembly_dataset_id.startswith(xlib.get_trinity_code()) and not assembly_dataset_id.startswith(xlib.get_star_code()) and not assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) and not assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
error_list.append('*** ERROR: the key "assembly_dataset_id" value is not a {0} nor {1} nor {2} nor {3} nor {4} nor {5} assembly.'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code()))
is_assembly_dataset_id_OK = False
OK = False
# check section "identification" - key "assembly_type"
assembly_type = busco_option_dict.get('identification', {}).get('assembly_type', not_found)
is_assembly_type_OK = True
if assembly_type == not_found:
error_list.append('*** ERROR: the key "assembly_type" is not found in the section "identification".')
is_assembly_type_OK = False
OK = False
elif assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
if assembly_type.upper() not in ['CONTIGS', 'SCAFFOLDS']:
error_list.append('*** ERROR: the key "assembly_type" must be "CONTIGS" or "SCAFFOLDS" when {0} is the assembly software.'.format(xlib.get_soapdenovotrans_name()))
is_assembly_type_OK = False
OK = False
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()) or assembly_dataset_id.startswith(xlib.get_trinity_code()) or assembly_dataset_id.startswith(xlib.get_star_code()) or assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) or assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
if assembly_type.upper() != 'NONE':
error_list.append('*** ERROR: the key "assembly_type" must be "NONE" when {0} or {1} or {2} or {3} or {4} is the assembly software.'.format(xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name()))
is_assembly_type_OK = False
OK = False
# check section "BUSCO parameters"
if 'BUSCO parameters' not in sections_list:
error_list.append('*** ERROR: the section "BUSCO parameters" is not found.')
OK = False
else:
# check section "BUSCO parameters" - key "ncpu"
ncpu = busco_option_dict.get('BUSCO parameters', {}).get('ncpu', not_found)
is_ncpu_OK = True
if ncpu == not_found:
error_list.append('*** ERROR: the key "ncpu" is not found in the section "BUSCO parameters".')
is_ncpu_OK = False
OK = False
else:
try:
if int(ncpu) < 1:
error_list.append('*** ERROR: the key "ncpu" in the section "BUSCO parameters" must be an integer value greater or equal to 1.')
is_ncpu_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "ncpu" in the section "BUSCO parameters" must be an integer value greater or equal to 1.')
is_ncpu_OK = False
OK = False
# check section "BUSCO parameters" - key "lineage_data"
lineage_data = busco_option_dict.get('BUSCO parameters', {}).get('lineage_data', not_found)
is_lineage_data_OK = True
if lineage_data == not_found:
error_list.append('*** ERROR: the key "lineage_data" is not found in the section "BUSCO parameters"')
is_lineage_data_OK = False
OK = False
# check section "BUSCO parameters" - key "mode"
mode = busco_option_dict.get('BUSCO parameters', {}).get('mode', not_found).lower()
is_mode_OK = True
if mode == not_found:
error_list.append('*** ERROR: the key "mode" is not found in the section "BUSCO parameters".')
is_mode_OK = False
OK = False
elif mode not in ['geno', 'tran', 'prot']:
error_list.append('*** ERROR: the key "mode" value in the section "BUSCO parameters" must be geno or tran or prot.')
is_mode_OK = False
OK = False
# check section "BUSCO parameters" - key "evalue"
evalue = busco_option_dict.get('BUSCO parameters', {}).get('evalue', not_found)
is_evalue_OK = True
if evalue == not_found:
error_list.append('*** ERROR: the key "evalue" is not found in the section "BUSCO parameters".')
is_evalue_OK = False
OK = False
else:
try:
if float(evalue) <= 0:
error_list.append('*** ERROR: the key "evalue" in the section "BUSCO parameters" must be a float value greater than 0.')
is_evalue_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "evalue" in the section "BUSCO parameters" must be a float value greater than 0.')
is_evalue_OK = False
OK = False
# check section "BUSCO parameters" - key "limit"
limit = busco_option_dict.get('BUSCO parameters', {}).get('limit', not_found)
is_limit_OK = True
if limit == not_found:
error_list.append('*** ERROR: the key "limit" is not found in the section "BUSCO parameters".')
OK = False
else:
try:
if int(limit) < 1:
error_list.append('*** ERROR: the key "limit" in the section "BUSCO parameters" must be an integer value greater or equal to 1.')
is_limit_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "limit" in the section "BUSCO parameters" must be an integer value greater or equal to 1.')
is_limit_OK = False
OK = False
# check section "BUSCO parameters" - key "species"
species = busco_option_dict.get('BUSCO parameters', {}).get('species', not_found)
is_species_OK = True
if species == not_found:
error_list.append('*** ERROR: the key "species" is not found in the section "BUSCO parameters"')
is_species_OK = False
OK = False
# check section "BUSCO parameters" - key "long"
long = busco_option_dict.get('BUSCO parameters', {}).get('long', not_found).upper()
is_long_OK = True
if long == not_found:
error_list.append('*** ERROR: the key "long" is not found in the section "BUSCO parameters".')
is_long_OK = False
OK = False
elif long not in ['YES', 'NO']:
error_list.append('*** ERROR: the key "long" value in the section "BUSCO parameters" must be YES or NO.')
is_long_OK = False
OK = False
# check section "BUSCO parameters" - key "augustus_options"
augustus_options = busco_option_dict.get('BUSCO parameters', {}).get('augustus_options', not_found)
is_augustus_options_OK = True
if augustus_options == not_found:
error_list.append('*** ERROR: the key "augustus_options" is not found in the section "BUSCO parameters".')
is_augustus_options_OK = False
OK = False
else:
if augustus_options.upper() != 'NONE':
parameter_list = [x.strip() for x in augustus_options.split(';')]
for parameter in parameter_list:
try:
if parameter.find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
except:
error_list.append('*** ERROR: the value of the key "augustus_options" in the section "BUSCO parameters" must be NONE or a valid August parameter list.')
is_augustus_options_OK = False
OK = False
break
# warn that the results config file is not valid if there are any errors
if not OK:
error_list.append('\nThe {0} config file is not valid. Please, correct this file or recreate it.'.format(xlib.get_busco_name()))
# return the control variable and the error list
return (OK, error_list)
def run_cd_hit_est_process(cluster_name, log, function=None):
'''
Run a CD-HIT-EST process.
'''
# initialize the control variable
OK = True
# get the CD-HIT-EST option dictionary
cd_hit_est_option_dict = xlib.get_option_dict(get_cd_hit_est_config_file())
# get the experiment identification
experiment_id = cd_hit_est_option_dict['identification']['experiment_id']
# warn that the log window must not be closed
if not isinstance(log, xlib.DevStdOut):
log.write(
'This process might take several minutes. Do not close this window, please wait!\n'
)
# validate the CD-HIT-EST config file
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Validating the {0} config file ...\n'.format(
xlib.get_cd_hit_est_name()))
(OK, error_list) = validate_cd_hit_est_config_file(strict=True)
if OK:
log.write('The config file is OK.\n')
else:
log.write('*** ERROR: The config file is not valid.\n')
log.write('Please correct this file or recreate the config files.\n')
# create the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Connecting the SSH client ...\n')
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(
cluster_name, 'master')
if OK:
log.write('The SSH client is connected.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# create the SSH transport connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Connecting the SSH transport ...\n')
(OK, error_list, ssh_transport) = xssh.create_ssh_transport_connection(
cluster_name, 'master')
if OK:
log.write('The SSH transport is connected.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# create the SFTP client
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Connecting the SFTP client ...\n')
sftp_client = xssh.create_sftp_client(ssh_transport)
log.write('The SFTP client is connected.\n')
# warn that the requirements are being verified
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Verifying process requirements ...\n')
# verify the master is running
if OK:
(master_state_code,
master_state_name) = xec2.get_node_state(cluster_name, 'master')
if master_state_code != 16:
log.write(
'*** ERROR: The cluster {0} is not running. Its state is {1} ({2}).\n'
.format(cluster_name, master_state_code, master_state_name))
OK = False
# verify the CD-HIT is set up
if OK:
(OK, error_list, is_setup) = xbioinfoapp.is_setup_bioconda_package(
xlib.get_cd_hit_bioconda_code(), cluster_name, True, ssh_client)
if OK:
if not is_setup:
log.write('*** ERROR: {0} is not setup.\n'.format(
xlib.get_cd_hit_name()))
OK = False
else:
log.write(
'*** ERROR: The verification of {0} setup could not be performed.\n'
.format(xlib.get_cd_hit_name()))
# warn that the requirements are OK
if OK:
log.write('Process requirements are OK.\n')
# determine the run directory in the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Determining the run directory in the cluster ...\n')
current_run_dir = xlib.get_cluster_current_run_dir(
experiment_id, xlib.get_cd_hit_est_code())
command = 'mkdir --parents {0}'.format(current_run_dir)
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write('The directory path is {0}.\n'.format(current_run_dir))
else:
log.write('*** ERROR: Wrong command ---> {0}\n'.format(command))
# build the CD-HIT-EST process script
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Building the process script {0} ...\n'.format(
get_cd_hit_est_process_script()))
(OK,
error_list) = build_cd_hit_est_process_script(cluster_name,
current_run_dir)
if OK:
log.write('The file is built.\n')
if not OK:
log.write('*** ERROR: The file could not be built.\n')
# upload the CD-HIT-EST process script to the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write(
'Uploading the process script {0} to the directory {1} of the master ...\n'
.format(get_cd_hit_est_process_script(), current_run_dir))
cluster_path = '{0}/{1}'.format(
current_run_dir, os.path.basename(get_cd_hit_est_process_script()))
(OK, error_list) = xssh.put_file(sftp_client,
get_cd_hit_est_process_script(),
cluster_path)
if OK:
log.write('The file is uploaded.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# set run permision to the CD-HIT-EST process script in the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Setting on the run permision of {0}/{1} ...\n'.format(
current_run_dir,
os.path.basename(get_cd_hit_est_process_script())))
command = 'chmod u+x {0}/{1}'.format(
current_run_dir, os.path.basename(get_cd_hit_est_process_script()))
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write('The run permision is set.\n')
else:
log.write('*** ERROR: Wrong command ---> {0}\n'.format(command))
# build the CD-HIT-EST process starter
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Building the process starter {0} ...\n'.format(
get_cd_hit_est_process_starter()))
(OK, error_list) = build_cd_hit_est_process_starter(current_run_dir)
if OK:
log.write('The file is built.\n')
if not OK:
log.write('***ERROR: The file could not be built.\n')
# upload the CD-HIT-EST process starter to the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write(
'Uploading the process starter {0} to the directory {1} of the master ...\n'
.format(get_cd_hit_est_process_starter(), current_run_dir))
cluster_path = '{0}/{1}'.format(
current_run_dir,
os.path.basename(get_cd_hit_est_process_starter()))
(OK, error_list) = xssh.put_file(sftp_client,
get_cd_hit_est_process_starter(),
cluster_path)
if OK:
log.write('The file is uploaded.\n')
else:
for error in error_list:
log.write('{0}\n'.format(error))
# set run permision to the CD-HIT-EST process starter in the cluster
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Setting on the run permision of {0}/{1} ...\n'.format(
current_run_dir,
os.path.basename(get_cd_hit_est_process_starter())))
command = 'chmod u+x {0}/{1}'.format(
current_run_dir,
os.path.basename(get_cd_hit_est_process_starter()))
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write('The run permision is set.\n')
else:
log.write('*** ERROR: Wrong command ---> {0}\n'.format(command))
# submit the CD-HIT-EST process
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Submitting the process script {0}/{1} ...\n'.format(
current_run_dir,
os.path.basename(get_cd_hit_est_process_starter())))
sge_env = xcluster.get_sge_env()
command = '{0}; qsub -V -b n -cwd {1}/{2}'.format(
sge_env, current_run_dir,
os.path.basename(get_cd_hit_est_process_starter()))
(OK, stdout,
stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
for line in stdout:
log.write('{0}\n'.format(line))
else:
log.write('*** ERROR: Wrong command ---> {0}\n'.format(command))
# close the SSH transport connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Closing the SSH transport connection ...\n')
xssh.close_ssh_transport_connection(ssh_transport)
log.write('The connection is closed.\n')
# close the SSH client connection
if OK:
log.write('{0}\n'.format(xlib.get_separator()))
log.write('Closing the SSH client connection ...\n')
xssh.close_ssh_client_connection(ssh_client)
log.write('The connection is closed.\n')
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write('{0}\n'.format(xlib.get_separator()))
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def get_result_dataset_dict(cluster_name, experiment_id, status, passed_connection, ssh_client):
'''
Get a dictionary with the result datasets of an experiment in the cluster.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the result directory in the cluster
cluster_result_dir = xlib.get_cluster_result_dir()
# initialize the dictionary of the result datasets
result_dataset_dict = {}
# create the SSH client connection
if not passed_connection:
(OK, error_list, ssh_client) = xssh.create_ssh_client_connection(cluster_name, 'master')
# verify the result directory is created
if OK:
command = '[ -d {0} ] && echo RC=0 || echo RC=1'.format(cluster_result_dir)
(OK, stdout, stderr) = xssh.execute_cluster_command(ssh_client, command)
if stdout[len(stdout) - 1] != 'RC=0':
error_list.append('*** ERROR: There is not any volume mounted in the result directory.\n')
error_list.append('You must link a volume in the mounting point {0} for the template {1}.\n'.format(cluster_result_dir, cluster_name))
OK = False
# get the dictionary of the result datasets
if OK:
if status == 'uncompressed':
command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'.format(cluster_result_dir, experiment_id)
elif status == 'compressed':
command = 'cd {0}/{1}; for list in `ls`; do ls -ld $list | grep -v ^d > /dev/null && echo $list; done;'.format(cluster_result_dir, experiment_id)
(OK, stdout, stderr) = xssh.execute_cluster_command(ssh_client, command)
if OK:
if status == 'uncompressed':
input_pattern = '{0}-(.+)-(.+)'
output_pattern = '{0} ({1} {2})'
elif status == 'compressed':
input_pattern = '{0}-(.+)-(.+).tar.gz'
output_pattern = '{0} ({1} {2}) [compressed]'
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id = line
if result_dataset_id.startswith(xlib.get_cd_hit_est_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_cd_hit_est_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_cd_hit_est_name(), date, time)
elif result_dataset_id.startswith(xlib.get_fastqc_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_fastqc_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_fastqc_name(), date, time)
elif result_dataset_id.startswith(xlib.get_gzip_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_gzip_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_gzip_name(), date, time)
elif result_dataset_id.startswith(xlib.get_insilico_read_normalization_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_insilico_read_normalization_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_insilico_read_normalization_name(), date, time)
elif result_dataset_id.startswith(xlib.get_quast_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_quast_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_quast_name(), date, time)
elif result_dataset_id.startswith(xlib.get_ref_eval_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_ref_eval_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_ref_eval_name(), date, time)
elif result_dataset_id.startswith(xlib.get_rnaquast_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_rnaquast_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_rnaquast_name(), date, time)
elif result_dataset_id.startswith(xlib.get_rsem_eval_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_rsem_eval_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_rsem_eval_name(), date, time)
elif result_dataset_id.startswith(xlib.get_soapdenovotrans_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_soapdenovotrans_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_soapdenovotrans_name(), date, time)
elif result_dataset_id.startswith(xlib.get_star_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_star_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_star_name(), date, time)
elif result_dataset_id.startswith(xlib.get_transabyss_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_transabyss_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_transabyss_name(), date, time)
elif result_dataset_id.startswith(xlib.get_transcript_filter_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_transcript_filter_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_transcript_filter_name(), date, time)
elif result_dataset_id.startswith(xlib.get_transcriptome_blastx_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_transcriptome_blastx_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_transcriptome_blastx_name(), date, time)
elif result_dataset_id.startswith(xlib.get_transrate_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_transrate_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_transrate_name(), date, time)
elif result_dataset_id.startswith(xlib.get_trimmomatic_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_trimmomatic_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_trimmomatic_name(), date, time)
elif result_dataset_id.startswith(xlib.get_trinity_code()+'-'):
mo = re.match(input_pattern.format(xlib.get_trinity_code()), result_dataset_id)
date = mo.group(1)
time = mo.group(2)
result_dataset_name = output_pattern.format(xlib.get_trinity_name(), date, time)
else:
result_dataset_name = result_dataset_id
result_dataset_dict[result_dataset_id] = {'result_dataset_id': result_dataset_id, 'result_dataset_name': result_dataset_name}
# close the SSH client connection
if OK and not passed_connection:
xssh.close_ssh_client_connection(ssh_client)
# return the control variable, error list and dictionary of the result datasets
return (OK, error_list, result_dataset_dict)
def create_cd_hit_est_config_file(experiment_id='exp001',
assembly_dataset_id='sdnt-170101-235959',
assembly_type='CONTIGS'):
'''
Create CD-HIT-EST config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the assembly software
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_star_code()):
assembly_software = xlib.get_star_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the CD-HIT-EST config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_cd_hit_est_config_file())):
os.makedirs(os.path.dirname(get_cd_hit_est_config_file()))
with open(get_cd_hit_est_config_file(), mode='w',
encoding='utf8') as file_id:
file_id.write('{0}\n'.format(
'# You must review the information of this file and update the values with the corresponding ones to the current run.'
))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format(
'# The assembly files must be located in the cluster directory {0}/experiment_id/assembly_dataset_id'
.format(xlib.get_cluster_result_dir())))
file_id.write('{0}\n'.format(
'# The experiment_id and assembly_dataset_id names are fixed in the identification section.'
))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format(
'# You can consult the parameters of CD-HIT-EST (CD-HIT package) and their meaning in http://weizhong-lab.ucsd.edu/cd-hit/.'
))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format(
'# In section "CD-HIT-EST parameters", the key "other_parameters" allows you to input additional parameters in the format:'
))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format(
'# other_parameters = --parameter-1[=value-1][; --parameter-2[=value-2][; ...; --parameter-n[=value-n]]]'
))
file_id.write('{0}\n'.format('#'))
file_id.write('{0}\n'.format(
'# parameter-i is a parameter name of CD-HIT-EST and value-i a valid value of parameter-i, e.g.'
))
file_id.write('{0}\n'.format('#'))
file_id.write(
'{0}\n'.format('# other_parameters = --aS=0.9; --U=10'))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format(
'# This section has the information identifies the assembly result dataset.'
))
file_id.write('{0}\n'.format('[identification]'))
file_id.write('{0:<50} {1}\n'.format(
'experiment_id = {0}'.format(experiment_id),
'# experiment identification'))
file_id.write('{0:<50} {1}\n'.format(
'assembly_software = {0}'.format(assembly_software),
'# assembly software: {0} ({1}) or {2} ({3}) or {4} ({5}) or {6} ({7}) or {8} ({9}) or {10} ({11})'
.format(xlib.get_soapdenovotrans_code(),
xlib.get_soapdenovotrans_name(),
xlib.get_transabyss_code(), xlib.get_transabyss_name(),
xlib.get_trinity_code(), xlib.get_trinity_name(),
xlib.get_star_code(), xlib.get_star_name(),
xlib.get_cd_hit_est_code(), xlib.get_cd_hit_est_name(),
xlib.get_transcript_filter_code(),
xlib.get_transcript_filter_name())))
file_id.write('{0:<50} {1}\n'.format(
'assembly_dataset_id = {0}'.format(assembly_dataset_id),
'# assembly dataset identification'))
file_id.write('{0:<50} {1}\n'.format(
'assembly_type = {0}'.format(assembly_type),
'# CONTIGS or SCAFFOLDS in {0}; NONE in {1}, {2}, {3}, {4} and {5}'
.format(xlib.get_soapdenovotrans_name(),
xlib.get_transabyss_name(), xlib.get_trinity_name(),
xlib.get_star_name(), xlib.get_cd_hit_est_name(),
xlib.get_transcript_filter_name())))
file_id.write('{0}\n'.format(''))
file_id.write('{0}\n'.format(
'# This section has the information to set the CD-HIT-EST parameters'
))
file_id.write('{0}\n'.format('[CD-HIT-EST parameters]'))
file_id.write('{0:<50} {1}\n'.format(
'threads = 2',
'# number of threads for use; with 0, all CPUs will be used'))
file_id.write('{0:<50} {1}\n'.format(
'memory_limit = 800',
'# memory limit (in MB) for the program; 0 for unlimitted'))
file_id.write('{0:<50} {1}\n'.format(
'seq_identity_threshold = 0.9',
'# sequence identity threshold'))
file_id.write('{0:<50} {1}\n'.format('word_length = 5',
'# word length'))
file_id.write('{0:<50} {1}\n'.format(
'mask = NX',
'# masking letters (e.g. -mask NX, to mask out both "N" and "X")'
))
file_id.write('{0:<50} {1}\n'.format(
'match = 2', '# matching score (1 for T-U and N-N)'))
file_id.write('{0:<50} {1}\n'.format('mismatch = -2',
'# mismatching score'))
file_id.write('{0:<50} {1}\n'.format(
'other_parameters = NONE',
'# additional parameters to the previous ones or NONE'))
except:
error_list.append(
'*** ERROR: The file {0} can not be recreated'.format(
get_cd_hit_est_config_file()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def create_express_config_file(experiment_id='exp001', assembly_dataset_id='sdnt-170101-235959', assembly_type='CONTIGS', alignment_dataset_id_list=['bowtie2-170101-235959']):
'''
Create eXpress config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the assembly software
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_ggtrinity_code()):
assembly_software = xlib.get_ggtrinity_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the eXpress config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_express_config_file())):
os.makedirs(os.path.dirname(get_express_config_file()))
with open(get_express_config_file(), mode='w', encoding='iso-8859-1', newline='\n') as file_id:
file_id.write( '# You must review the information of this file and update the values with the corresponding ones to the current run.\n')
file_id.write( '#\n')
file_id.write(f'# The assembly files have to be located in the cluster directory {xlib.get_cluster_result_dir()}/experiment_id/assembly_dataset_id\n')
file_id.write(f'# The alignment file has to be located in the cluster directory {xlib.get_cluster_result_dir()}/experiment_id/alignment_dataset_id\n')
file_id.write( '# The experiment_id, assembly_dataset_id and alignment_dataset_id are fixed in the identification section.\n')
file_id.write( '#\n')
file_id.write( '# You can consult the parameters of eXpress and their meaning in "https://pachterlab.github.io/eXpress/".\n')
file_id.write( '#\n')
file_id.write( '# In section "eXpress parameters", the key "other_parameters" allows you to input additional parameters in the format:\n')
file_id.write( '#\n')
file_id.write( '# other_parameters = --parameter-1[=value-1][; --parameter-2[=value-2][; ...; --parameter-n[=value-n]]]\n')
file_id.write( '#\n')
file_id.write( '# parameter-i is a parameter name of Cufflinks and value-i a valid value of parameter-i, e.g.\n')
file_id.write( '#\n')
file_id.write( '# other_parameters = --calc-covar; --forget-param=0.6\n')
file_id.write( '\n')
file_id.write( '# This section has the information identifies the experiment.\n')
file_id.write( '[identification]\n')
file_id.write( '{0:<50} {1}\n'.format(f'experiment_id = {experiment_id}', '# experiment identification'))
file_id.write( '{0:<50} {1}\n'.format(f'assembly_software = {assembly_software}', f'# assembly software: {get_assembly_software_code_list_text()}'))
file_id.write( '{0:<50} {1}\n'.format(f'assembly_dataset_id = {assembly_dataset_id}', '# assembly dataset identification'))
file_id.write( '{0:<50} {1}\n'.format(f'assembly_type = {assembly_type}', f'# assembly type: CONTIGS or SCAFFOLDS in {xlib.get_soapdenovotrans_name()}; NONE in any other case'))
for i in range(len(alignment_dataset_id_list)):
# set the alignment software
alignment_dataset_id = alignment_dataset_id_list[i]
if alignment_dataset_id.startswith(xlib.get_bowtie2_code()):
alignment_software = xlib.get_bowtie2_code()
elif alignment_dataset_id.startswith(xlib.get_gsnap_code()):
alignment_software = xlib.get_gsnap_code()
# write the alignment dataset section
file_id.write( '\n')
if i == 0:
file_id.write( '# This section has the information of the first alignment dataset.\n')
file_id.write(f'[alignment-dataset-{i + 1}]\n')
file_id.write( '{0:<50} {1}\n'.format(f'alignment_software = {alignment_software}', f'# alignment software: {get_alignment_software_code_list_text()}'))
file_id.write( '{0:<50} {1}\n'.format(f'alignment_dataset_id = {alignment_dataset_id}', '# alignment dataset identification'))
if i == 0:
file_id.write( '\n')
file_id.write( '# If there are more alignment datasets, you have to repeat the section alignment-dataset-1 with the data of each dataset.\n')
file_id.write( '# The section identification has to be alignment-dataset-n (n is an integer not repeated)\n')
file_id.write( '\n')
file_id.write( '# This section has the information to set the eXpress parameters\n')
file_id.write( '[eXpress parameters]\n')
file_id.write( '{0:<50} {1}\n'.format( 'frag-len-mean = 200', '# mean fragment length'))
file_id.write( '{0:<50} {1}\n'.format( 'frag-len-stddev = 60', '# fragment length standard deviation'))
file_id.write( '{0:<50} {1}\n'.format( 'library_type = NONE', f'# library type: {get_library_type_code_list_text()}'))
file_id.write( '{0:<50} {1}\n'.format( 'max-indel-size = 0', '# maximum allowed size of a single indel'))
file_id.write( '{0:<50} {1}\n'.format( 'no-bias-correct = NO', f'# if YES, eXpress will not measure and account for sequence-specific biases: {get_no_bias_correct_code_list_text()}'))
file_id.write( '{0:<50} {1}\n'.format( 'no-error-model = NO', f'# if YES, eXpress will not measure and account for errors in alignments: {get_no_error_model_code_list_text()}'))
file_id.write( '{0:<50} {1}\n'.format( 'other_parameters = NONE', '# additional parameters to the previous ones or NONE'))
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append(f'*** ERROR: The file {get_express_config_file()} can not be recreated')
OK = False
# return the control variable and the error list
return (OK, error_list)
def build_cd_hit_est_process_script(cluster_name, current_run_dir):
'''
Build the current CD-HIT-EST process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the option dictionary
cd_hit_est_option_dict = xlib.get_option_dict(get_cd_hit_est_config_file())
# get the options
experiment_id = cd_hit_est_option_dict['identification']['experiment_id']
assembly_software = cd_hit_est_option_dict['identification'][
'assembly_software']
assembly_dataset_id = cd_hit_est_option_dict['identification'][
'assembly_dataset_id']
assembly_type = cd_hit_est_option_dict['identification']['assembly_type']
threads = cd_hit_est_option_dict['CD-HIT-EST parameters']['threads']
memory_limit = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'memory_limit']
seq_identity_threshold = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'seq_identity_threshold']
word_length = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'word_length']
mask = cd_hit_est_option_dict['CD-HIT-EST parameters']['mask']
match = cd_hit_est_option_dict['CD-HIT-EST parameters']['match']
mismatch = cd_hit_est_option_dict['CD-HIT-EST parameters']['mismatch']
other_parameters = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'other_parameters']
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type == 'CONTIGS':
transcriptome_file = '{0}/{1}-{2}.contig'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id), experiment_id,
assembly_dataset_id)
elif assembly_type == 'SCAFFOLDS':
transcriptome_file = '{0}/{1}-{2}.scafSeq'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id), experiment_id,
assembly_dataset_id)
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = '{0}/transabyss-final.fa'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = '{0}/Trinity.fasta'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_star_code():
transcriptome_file = '{0}/Trinity-GG.fasta'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = '{0}/clustered-transcriptome.fasta'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = '{0}/filtered-transcriptome.fasta'.format(
xlib.get_cluster_experiment_result_dataset_dir(
experiment_id, assembly_dataset_id))
# set the output file path
if OK:
output_file = '{0}/clustered-transcriptome.fasta'.format(
current_run_dir)
# write the CD-HIT-EST process script
try:
if not os.path.exists(os.path.dirname(
get_cd_hit_est_process_script())):
os.makedirs(os.path.dirname(get_cd_hit_est_process_script()))
with open(get_cd_hit_est_process_script(),
mode='w',
encoding='utf8',
newline='\n') as file_id:
file_id.write('{0}\n'.format('#!/bin/bash'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format(
'CDHIT_PATH={0}/{1}/envs/{2}/bin'.format(
xlib.get_cluster_app_dir(), xlib.get_miniconda3_name(),
xlib.get_cd_hit_bioconda_code())))
file_id.write('{0}\n'.format('PATH=$CDHIT_PATH:$PATH'))
file_id.write('{0}\n'.format(
'SEP="#########################################"'))
file_id.write('{0}\n'.format('cd {0}/{1}/bin'.format(
xlib.get_cluster_app_dir(), xlib.get_miniconda3_name())))
file_id.write('{0}\n'.format('source activate {0}'.format(
xlib.get_cd_hit_bioconda_code())))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('function init'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' INIT_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(
' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`'
))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(
' echo "Script started in node $HOSTNAME of cluster {0} at $FORMATTED_INIT_DATETIME UTC."'
.format(cluster_name)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('function run_cd_hit_est_process'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(
' echo "Running {0} process ..."'.format(
xlib.get_cd_hit_est_name())))
file_id.write('{0}\n'.format(' /usr/bin/time \\'))
file_id.write('{0}\n'.format(
' --format="$SEP\\nElapsed real time (s): %e\\nCPU time in kernel mode (s): %S\\nCPU time in user mode (s): %U\\nPercentage of CPU: %P\\nMaximum resident set size(Kb): %M\\nAverage total memory use (Kb):%K" \\'
))
file_id.write('{0}\n'.format(' cd-hit-est \\'))
file_id.write('{0}\n'.format(
' -T {0} \\'.format(threads)))
file_id.write('{0}\n'.format(
' -M {0} \\'.format(memory_limit)))
file_id.write('{0}\n'.format(
' -i {0} \\'.format(transcriptome_file)))
file_id.write('{0}\n'.format(
' -c {0} \\'.format(seq_identity_threshold)))
file_id.write('{0}\n'.format(
' -n {0} \\'.format(word_length)))
file_id.write('{0}\n'.format(
' -mask {0} \\'.format(mask)))
file_id.write('{0}\n'.format(
' -match {0} \\'.format(match)))
file_id.write('{0}\n'.format(
' -mismatch {0} \\'.format(mismatch)))
if other_parameters.upper() == 'NONE':
file_id.write('{0}\n'.format(
' -o {0}'.format(output_file)))
else:
file_id.write('{0}\n'.format(
' -o {0} \\'.format(output_file)))
parameter_list = [
x.strip() for x in other_parameters.split(';')
]
for i in range(len(parameter_list)):
if parameter_list[i].find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
if i < len(parameter_list) - 1:
file_id.write('{0}\n'.format(
' -{0} {1} \\'.format(
parameter_name, parameter_value)))
else:
file_id.write('{0}\n'.format(
' -{0} {1}'.format(
parameter_name, parameter_value)))
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
if i < len(parameter_list):
file_id.write('{0}\n'.format(
' -{0} \\'.format(parameter_name)))
else:
file_id.write('{0}\n'.format(
' -{0}'.format(parameter_name)))
i += 1
file_id.write('{0}\n'.format(' RC=$?'))
file_id.write('{0}\n'.format(
' if [ $RC -ne 0 ]; then manage_error cd-hit-est $RC; fi'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('function end'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'
))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(
' echo "Script ended OK at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'
))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(
xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(
' SUBJECT="{0}: {1} process"'.format(
xlib.get_project_name(), xlib.get_cd_hit_est_name())))
file_id.write('{0}\n'.format(
' MESSAGE="The {0} process in node $HOSTNAME of cluster {0} ended OK at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'
.format(xlib.get_rsem_eval_name(), cluster_name)))
file_id.write('{0}\n'.format(
' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'
))
file_id.write('{0}\n'.format(' exit 0'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('function manage_error'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'
))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write(
'{0}\n'.format(' echo "ERROR: $1 returned error $2"'))
file_id.write('{0}\n'.format(
' echo "Script ended WRONG at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'
))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(
xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(
' SUBJECT="{0}: {1} process"'.format(
xlib.get_project_name(), xlib.get_cd_hit_est_name())))
file_id.write('{0}\n'.format(
' MESSAGE="The {0} process in node $HOSTNAME of cluster {0} ended WRONG at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'
.format(xlib.get_rsem_eval_name(), cluster_name)))
file_id.write('{0}\n'.format(
' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'
))
file_id.write('{0}\n'.format(' exit 3'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('function calculate_duration'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(
' DURATION=`expr $END_DATETIME - $INIT_DATETIME`'))
file_id.write('{0}\n'.format(' HH=`expr $DURATION / 3600`'))
file_id.write(
'{0}\n'.format(' MM=`expr $DURATION % 3600 / 60`'))
file_id.write('{0}\n'.format(' SS=`expr $DURATION % 60`'))
file_id.write('{0}\n'.format(
' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`'
))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format(
'#-------------------------------------------------------------------------------'
))
file_id.write('{0}\n'.format('init'))
file_id.write('{0}\n'.format('run_cd_hit_est_process'))
file_id.write('{0}\n'.format('end'))
except:
error_list.append('*** ERROR: The file {0} can not be created'.format(
get_cd_hit_est_process_script()))
OK = False
# return the control variable and the error list
return (OK, error_list)
def build_express_process_script(cluster_name, current_run_dir):
'''
Build the current eXpress process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the eXpress option dictionary
express_option_dict = xlib.get_option_dict(get_express_config_file())
# get the options
experiment_id = express_option_dict['identification']['experiment_id']
assembly_software = express_option_dict['identification']['assembly_software']
assembly_dataset_id = express_option_dict['identification']['assembly_dataset_id']
assembly_type = express_option_dict['identification']['assembly_type']
frag_len_mean = express_option_dict['eXpress parameters']['frag-len-mean']
frag_len_stddev = express_option_dict['eXpress parameters']['frag-len-stddev']
library_type = express_option_dict['eXpress parameters']['library_type']
max_indel_size = express_option_dict['eXpress parameters']['max-indel-size']
no_bias_correct = express_option_dict['eXpress parameters']['no-bias-correct']
no_error_model = express_option_dict['eXpress parameters']['no-error-model']
other_parameters = express_option_dict['eXpress parameters']['other_parameters']
# get the sections list
sections_list = []
for section in express_option_dict.keys():
sections_list.append(section)
sections_list.sort()
# build alignment dataset identification list
alignment_software_list = []
alignment_dataset_id_list = []
for section in sections_list:
# if the section identification is like library-n
if re.match('^alignment-dataset-[0-9]+$', section):
alignment_software_list.append(express_option_dict[section]['alignment_software'])
alignment_dataset_id_list.append(express_option_dict[section]['alignment_dataset_id'])
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type == 'CONTIGS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.contig'
elif assembly_type == 'SCAFFOLDS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.scafSeq'
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/transabyss-final.fa'
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity.fasta'
elif assembly_software == xlib.get_ggtrinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity-GG.fasta'
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/clustered-transcriptome.fasta'
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/filtered-transcriptome.fasta'
# write the eXpress process script
try:
if not os.path.exists(os.path.dirname(get_express_process_script())):
os.makedirs(os.path.dirname(get_express_process_script()))
with open(get_express_process_script(), mode='w', encoding='iso-8859-1', newline='\n') as script_file_id:
script_file_id.write( '#!/bin/bash\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'SEP="#########################################"\n')
script_file_id.write( 'export HOST_IP=`curl --silent checkip.amazonaws.com`\n')
script_file_id.write( 'export HOST_ADDRESS="ec2-${HOST_IP//./-}-compute-1.amazonaws.com"\n')
script_file_id.write( 'export AWS_CONFIG_FILE=/home/ubuntu/.aws/config\n')
script_file_id.write( 'export AWS_SHARED_CREDENTIALS_FILE=/home/ubuntu/.aws/credentials\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write(f'MINICONDA3_BIN_PATH={xlib.get_cluster_app_dir()}/{xlib.get_miniconda3_name()}/bin\n')
script_file_id.write(f'export PATH=$MINICONDA3_BIN_PATH:$PATH\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write(f'CURRENT_DIR={current_run_dir}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write(f'STATUS_DIR={xlib.get_status_dir(current_run_dir)}\n')
script_file_id.write(f'SCRIPT_STATUS_OK={xlib.get_status_ok(current_run_dir)}\n')
script_file_id.write(f'SCRIPT_STATUS_WRONG={xlib.get_status_wrong(current_run_dir)}\n')
script_file_id.write( 'mkdir --parents $STATUS_DIR\n')
script_file_id.write( 'if [ -f $SCRIPT_STATUS_OK ]; then rm $SCRIPT_STATUS_OK; fi\n')
script_file_id.write( 'if [ -f $SCRIPT_STATUS_WRONG ]; then rm $SCRIPT_STATUS_WRONG; fi\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'function init\n')
script_file_id.write( '{\n')
script_file_id.write( ' INIT_DATETIME=`date --utc +%s`\n')
script_file_id.write( ' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write( ' echo "Script started at $FORMATTED_INIT_DATETIME+00:00."\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write(f' echo "CLUSTER: {cluster_name}"\n')
script_file_id.write( ' echo "HOST NAME: $HOSTNAME"\n')
script_file_id.write( ' echo "HOST IP: $HOST_IP"\n')
script_file_id.write( ' echo "HOST ADDRESS: $HOST_ADDRESS"\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'function run_express_process\n')
script_file_id.write( '{\n')
script_file_id.write(f' source activate {xlib.get_express_anaconda_code()}\n')
script_file_id.write(f' cd $CURRENT_DIR\n')
for i in range(len(alignment_dataset_id_list)):
alignment_files = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, alignment_dataset_id_list[i])}/*.sorted.bam'
script_file_id.write(f' SORTED_BAM_LIST={alignment_dataset_id_list[i]}-sorted-bam-files.txt\n')
script_file_id.write(f' ls {alignment_files} > $SORTED_BAM_LIST\n')
script_file_id.write( ' while read FILE_BAM; do\n')
script_file_id.write( ' NAME=`basename $FILE_BAM`\n')
script_file_id.write( ' NAME=${NAME:0:-11}\n')
script_file_id.write(f' SUBDIR={alignment_dataset_id_list[i]}-$NAME\n')
script_file_id.write(f' mkdir --parents $CURRENT_DIR/$SUBDIR\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write(f' echo "Quantitating alignment dataset {alignment_dataset_id_list[i]} - library $SUBDIR ..."\n')
script_file_id.write( ' /usr/bin/time \\\n')
script_file_id.write(f' --format="{xlib.get_time_output_format(separator=False)}" \\\n')
script_file_id.write( ' express \\\n')
script_file_id.write( ' --no-update-check \\\n')
script_file_id.write(f' --frag-len-mean {frag_len_mean} \\\n')
script_file_id.write(f' --frag-len-stddev {frag_len_stddev} \\\n')
if library_type.lower() == 'fr-stranded':
script_file_id.write( ' --fr-stranded \\\n')
elif library_type.lower() == 'rf-stranded':
script_file_id.write( ' --rf-stranded \\\n')
elif library_type.lower() == 'f-stranded':
script_file_id.write( ' --f-stranded \\\n')
elif library_type.lower() == 'r-stranded':
script_file_id.write( ' --r-stranded \\\n')
script_file_id.write(f' --max-indel-size {max_indel_size} \\\n')
if no_bias_correct.upper() == 'YES':
script_file_id.write( ' --no-bias-correct \\\n')
if no_error_model.upper() == 'YES':
script_file_id.write( ' --no-error-model \\\n')
if other_parameters.upper() != 'NONE':
parameter_list = [x.strip() for x in other_parameters.split(';')]
for i in range(len(parameter_list)):
if parameter_list[i].find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
script_file_id.write(f' --{parameter_name}={parameter_value} \\\n')
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
script_file_id.write(f' --{parameter_name} \\\n')
script_file_id.write( ' --output-dir $CURRENT_DIR/$SUBDIR \\\n')
script_file_id.write(f' {transcriptome_file} \\\n')
script_file_id.write( ' $FILE_BAM\n')
script_file_id.write( ' RC=$?\n')
script_file_id.write( ' if [ $RC -ne 0 ]; then manage_error express $RC; fi\n')
script_file_id.write( ' echo "Quantitation is done."\n')
script_file_id.write( ' done < $SORTED_BAM_LIST\n')
script_file_id.write( ' conda deactivate\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'function end\n')
script_file_id.write( '{\n')
script_file_id.write( ' END_DATETIME=`date --utc +%s`\n')
script_file_id.write( ' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n')
script_file_id.write( ' calculate_duration\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write( ' echo "Script ended OK at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write( ' send_mail ok\n')
script_file_id.write( ' touch $SCRIPT_STATUS_OK\n')
script_file_id.write( ' exit 0\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'function manage_error\n')
script_file_id.write( '{\n')
script_file_id.write( ' END_DATETIME=`date --utc +%s`\n')
script_file_id.write( ' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n')
script_file_id.write( ' calculate_duration\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write( ' echo "ERROR: $1 returned error $2"\n')
script_file_id.write( ' echo "Script ended WRONG at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n')
script_file_id.write( ' echo "$SEP"\n')
script_file_id.write( ' send_mail wrong\n')
script_file_id.write( ' touch $SCRIPT_STATUS_WRONG\n')
script_file_id.write( ' exit 3\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
process_name = f'{xlib.get_express_name()} process'
mail_message_ok = xlib.get_mail_message_ok(process_name, cluster_name)
mail_message_wrong = xlib.get_mail_message_wrong(process_name, cluster_name)
script_file_id.write( 'function send_mail\n')
script_file_id.write( '{\n')
script_file_id.write(f' SUBJECT="{xlib.get_project_name()}: {process_name}"\n')
script_file_id.write( ' if [ "$1" == "ok" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_ok}"\n')
script_file_id.write( ' elif [ "$1" == "wrong" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_wrong}"\n')
script_file_id.write( ' else\n')
script_file_id.write( ' MESSAGE=""\n')
script_file_id.write( ' fi\n')
script_file_id.write( ' DESTINATION_FILE=mail-destination.json\n')
script_file_id.write( ' echo "{" > $DESTINATION_FILE\n')
script_file_id.write(f' echo " \\\"ToAddresses\\\": [\\\"{xconfiguration.get_contact_data()}\\\"]," >> $DESTINATION_FILE\n')
script_file_id.write( ' echo " \\\"CcAddresses\\\": []," >> $DESTINATION_FILE\n')
script_file_id.write( ' echo " \\\"BccAddresses\\\": []" >> $DESTINATION_FILE\n')
script_file_id.write( ' echo "}" >> $DESTINATION_FILE\n')
script_file_id.write( ' MESSAGE_FILE=mail-message.json\n')
script_file_id.write( ' echo "{" > $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Subject\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Data\\\": \\\"$SUBJECT\\\"," >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " }," >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Body\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Html\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Data\\\": \\\"$MESSAGE\\\"," >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write( ' echo "}" >> $MESSAGE_FILE\n')
script_file_id.write(f' aws ses send-email --from {xconfiguration.get_contact_data()} --destination file://$DESTINATION_FILE --message file://$MESSAGE_FILE\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'function calculate_duration\n')
script_file_id.write( '{\n')
script_file_id.write( ' DURATION=`expr $END_DATETIME - $INIT_DATETIME`\n')
script_file_id.write( ' HH=`expr $DURATION / 3600`\n')
script_file_id.write( ' MM=`expr $DURATION % 3600 / 60`\n')
script_file_id.write( ' SS=`expr $DURATION % 60`\n')
script_file_id.write( ' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`\n')
script_file_id.write( '}\n')
script_file_id.write( '#-------------------------------------------------------------------------------\n')
script_file_id.write( 'init\n')
script_file_id.write( 'run_express_process\n')
script_file_id.write( 'end\n')
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append(f'*** ERROR: The file {get_express_process_script()} can not be created')
OK = False
# return the control variable and the error list
return (OK, error_list)
def create_busco_config_file(experiment_id='exp001',
assembly_dataset_id='sdnt-170101-235959',
assembly_type='CONTIGS'):
'''
Create BUSCO config file with the default options. It is necessary
update the options in each run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# set the assembly software
if assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
assembly_software = xlib.get_soapdenovotrans_code()
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()):
assembly_software = xlib.get_transabyss_code()
elif assembly_dataset_id.startswith(xlib.get_trinity_code()):
assembly_software = xlib.get_trinity_code()
elif assembly_dataset_id.startswith(xlib.get_ggtrinity_code()):
assembly_software = xlib.get_ggtrinity_code()
elif assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()):
assembly_software = xlib.get_cd_hit_est_code()
elif assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
assembly_software = xlib.get_transcript_filter_code()
# create the BUSCO config file and write the default options
try:
if not os.path.exists(os.path.dirname(get_busco_config_file())):
os.makedirs(os.path.dirname(get_busco_config_file()))
with open(get_busco_config_file(),
mode='w',
encoding='iso-8859-1',
newline='\n') as file_id:
file_id.write(
'# You must review the information of this file and update the values with the corresponding ones to the current run.\n'
)
file_id.write('#\n')
file_id.write(
f'# The reference file has to be located in the cluster directory {xlib.get_cluster_reference_dir()}/experiment_id/reference_dataset_id\n'
)
file_id.write(
f'# The assembly files have to be located in the cluster directory {xlib.get_cluster_result_dir()}/experiment_id/assembly_dataset_id\n'
)
file_id.write(
'# The experiment_id and assembly_dataset_id names are fixed in the identification section.\n'
)
file_id.write('#\n')
file_id.write(
'# In section "BUSCO parameters", the key "augustus_options" allows you to input additional August parameters in the format:\n'
)
file_id.write('#\n')
file_id.write(
'# augustus_options = --parameter-1[=value-1][; --parameter-2[=value-2][; ...; --parameter-n[=value-n]]]\n'
)
file_id.write('#\n')
file_id.write(
'# parameter-i is a parameter name of Augustus and value-i a valid value of parameter-i, e.g.\n'
)
file_id.write('#\n')
file_id.write(
'# augustus_options = --translation_table=6 --progress=true\n'
)
file_id.write('#\n')
file_id.write(
'# You can consult the parameters of BUSCO and their meaning in "http://busco.ezlab.org/"\n'
)
file_id.write(
'# and the ones of August in "http://bioinf.uni-greifswald.de/augustus/".\n'
)
file_id.write('\n')
file_id.write(
'# This section has the information identifies the experiment.\n'
)
file_id.write('[identification]\n')
file_id.write('{0:<50} {1}\n'.format(
f'experiment_id = {experiment_id}',
'# experiment identification'))
file_id.write('{0:<50} {1}\n'.format(
f'assembly_software = {assembly_software}',
f'# assembly software: {get_assembly_software_code_list_text()}'
))
file_id.write('{0:<50} {1}\n'.format(
f'assembly_dataset_id = {assembly_dataset_id}',
'# assembly dataset identification'))
file_id.write('{0:<50} {1}\n'.format(
f'assembly_type = {assembly_type}',
f'# assembly type: CONTIGS or SCAFFOLDS in {xlib.get_soapdenovotrans_name()}; NONE in any other case'
))
file_id.write('\n')
file_id.write(
'# This section has the information to set the BUSCO parameters\n'
)
file_id.write('[BUSCO parameters]\n')
file_id.write('{0:<50} {1}\n'.format(
'ncpu = 4', '# number of threads/cores for use'))
file_id.write('{0:<50} {1}\n'.format(
'lineage_data_url = https://busco-data.ezlab.org/v4/data/lineages/viridiplantae_odb10.2020-09-10.tar.gz',
'# the url of lineage data file that will be used'))
file_id.write('{0:<50} {1}\n'.format(
'mode = TRAN', f'# mode: {get_mode_code_list_text()}'))
file_id.write('{0:<50} {1}\n'.format(
'evalue = 1E-03', '# E-value cutoff for BLAST searches'))
file_id.write('{0:<50} {1}\n'.format(
'limit = 3', '# number of candidate regions to consider'))
file_id.write('{0:<50} {1}\n'.format(
'species = NONE',
'# identifier of existing Augustus species gene finding parameters or NONE'
))
file_id.write('{0:<50} {1}\n'.format(
'long = NO',
f'# Augustus optimization mode for self-training: {get_long_code_list_text()}'
))
file_id.write('{0:<50} {1}\n'.format(
'augustus_options = NONE',
'# additional parameters to August or NONE'))
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append(
f'*** ERROR: The file {get_busco_config_file()} can not be recreated'
)
OK = False
# return the control variable and the error list
return (OK, error_list)
def run_cd_hit_est_process(cluster_name, log, function=None):
'''
Run a CD-HIT-EST process.
'''
# initialize the control variable
OK = True
# get the CD-HIT-EST option dictionary
cd_hit_est_option_dict = xlib.get_option_dict(get_cd_hit_est_config_file())
# get the experiment identification
experiment_id = cd_hit_est_option_dict['identification']['experiment_id']
# warn that the log window does not have to be closed
if not isinstance(log, xlib.DevStdOut):
log.write(
'This process might take several minutes. Do not close this window, please wait!\n'
)
# check the CD-HIT-EST config file
log.write(f'{xlib.get_separator()}\n')
log.write(f'Checking the {xlib.get_cd_hit_est_name()} config file ...\n')
(OK, error_list) = check_cd_hit_est_config_file(strict=True)
if OK:
log.write('The file is OK.\n')
else:
log.write('*** ERROR: The config file is not valid.\n')
log.write('Please correct this file or recreate the config files.\n')
# create the SSH client connection
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Connecting the SSH client ...\n')
(OK, error_list,
ssh_client) = xssh.create_ssh_client_connection(cluster_name)
if OK:
log.write('The SSH client is connected.\n')
else:
for error in error_list:
log.write(f'{error}\n')
# create the SSH transport connection
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Connecting the SSH transport ...\n')
(OK, error_list,
ssh_transport) = xssh.create_ssh_transport_connection(cluster_name)
if OK:
log.write('The SSH transport is connected.\n')
else:
for error in error_list:
log.write(f'{error}\n')
# create the SFTP client
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Connecting the SFTP client ...\n')
sftp_client = xssh.create_sftp_client(ssh_transport)
log.write('The SFTP client is connected.\n')
# warn that the requirements are being verified
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Checking process requirements ...\n')
# check the master is running
if OK:
(master_state_code,
master_state_name) = xec2.get_node_state(cluster_name)
if master_state_code != 16:
log.write(
f'*** ERROR: The cluster {cluster_name} is not running. Its state is {master_state_code} ({master_state_name}).\n'
)
OK = False
# check the CD-HIT is installed
if OK:
(OK, error_list,
is_installed) = xbioinfoapp.is_installed_anaconda_package(
xlib.get_cd_hit_anaconda_code(), cluster_name, True, ssh_client)
if OK:
if not is_installed:
log.write(
f'*** ERROR: {xlib.get_cd_hit_name()} is not installed.\n')
OK = False
else:
log.write(
f'*** ERROR: The verification of {xlib.get_cd_hit_name()} installation could not be performed.\n'
)
# warn that the requirements are OK
if OK:
log.write('Process requirements are OK.\n')
# determine the run directory in the cluster
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Determining the run directory in the cluster ...\n')
current_run_dir = xlib.get_cluster_current_run_dir(
experiment_id, xlib.get_cd_hit_est_code())
command = f'mkdir --parents {current_run_dir}'
(OK, _, _) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write(f'The directory path is {current_run_dir}.\n')
else:
log.write(f'*** ERROR: Wrong command ---> {command}\n')
# build the CD-HIT-EST process script
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Building the process script {get_cd_hit_est_process_script()} ...\n'
)
(OK,
error_list) = build_cd_hit_est_process_script(cluster_name,
current_run_dir)
if OK:
log.write('The file is built.\n')
if not OK:
log.write('*** ERROR: The file could not be built.\n')
# upload the CD-HIT-EST process script to the cluster
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Uploading the process script {get_cd_hit_est_process_script()} to the directory {current_run_dir} ...\n'
)
cluster_path = f'{current_run_dir}/{os.path.basename(get_cd_hit_est_process_script())}'
(OK, error_list) = xssh.put_file(sftp_client,
get_cd_hit_est_process_script(),
cluster_path)
if OK:
log.write('The file is uploaded.\n')
else:
for error in error_list:
log.write(f'{error}\n')
# set run permision to the CD-HIT-EST process script in the cluster
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Setting on the run permision of {current_run_dir}/{os.path.basename(get_cd_hit_est_process_script())} ...\n'
)
command = f'chmod u+x {current_run_dir}/{os.path.basename(get_cd_hit_est_process_script())}'
(OK, _, _) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write('The run permision is set.\n')
else:
log.write(f'*** ERROR: Wrong command ---> {command}\n')
# build the CD-HIT-EST process starter
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Building the process starter {get_cd_hit_est_process_starter()} ...\n'
)
(OK, error_list) = build_cd_hit_est_process_starter(current_run_dir)
if OK:
log.write('The file is built.\n')
if not OK:
log.write('***ERROR: The file could not be built.\n')
# upload the CD-HIT-EST process starter to the cluster
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Uploading the process starter {get_cd_hit_est_process_starter()} to the directory {current_run_dir} ...\n'
)
cluster_path = f'{current_run_dir}/{os.path.basename(get_cd_hit_est_process_starter())}'
(OK, error_list) = xssh.put_file(sftp_client,
get_cd_hit_est_process_starter(),
cluster_path)
if OK:
log.write('The file is uploaded.\n')
else:
for error in error_list:
log.write(f'{error}\n')
# set run permision to the CD-HIT-EST process starter in the cluster
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Setting on the run permision of {current_run_dir}/{os.path.basename(get_cd_hit_est_process_starter())} ...\n'
)
command = f'chmod u+x {current_run_dir}/{os.path.basename(get_cd_hit_est_process_starter())}'
(OK, _, _) = xssh.execute_cluster_command(ssh_client, command)
if OK:
log.write('The run permision is set.\n')
else:
log.write(f'*** ERROR: Wrong command ---> {command}\n')
# submit the CD-HIT-EST process
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write(
f'Submitting the process script {current_run_dir}/{os.path.basename(get_cd_hit_est_process_starter())} ...\n'
)
OK = xssh.submit_script(
cluster_name, ssh_client, current_run_dir,
os.path.basename(get_cd_hit_est_process_starter()), log)
# close the SSH transport connection
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Closing the SSH transport connection ...\n')
xssh.close_ssh_transport_connection(ssh_transport)
log.write('The connection is closed.\n')
# close the SSH client connection
if OK:
log.write(f'{xlib.get_separator()}\n')
log.write('Closing the SSH client connection ...\n')
xssh.close_ssh_client_connection(ssh_client)
log.write('The connection is closed.\n')
# warn that the log window can be closed
if not isinstance(log, xlib.DevStdOut):
log.write(f'{xlib.get_separator()}\n')
log.write('You can close this window now.\n')
# execute final function
if function is not None:
function()
# return the control variable
return OK
def validate_gmap_config_file(strict):
'''
Validate the GMAP config file of a run.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# intitialize variable used when value is not found
not_found = '***NOTFOUND***'.upper()
# get the option dictionary
try:
gmap_option_dict = xlib.get_option_dict(get_gmap_config_file())
except:
error_list.append('*** ERROR: The syntax is WRONG.')
OK = False
else:
# get the sections list
sections_list = []
for section in gmap_option_dict.keys():
sections_list.append(section)
sections_list.sort()
# check section "identification"
if 'identification' not in sections_list:
error_list.append('*** ERROR: the section "identification" is not found.')
OK = False
else:
# check section "identification" - key "experiment_id"
experiment_id = gmap_option_dict.get('identification', {}).get('experiment_id', not_found)
is_experiment_id_OK = True
if experiment_id == not_found:
error_list.append('*** ERROR: the key "experiment_id" is not found in the section "identification".')
is_experiment_id_OK = False
OK = False
# check section "identification" - key "reference_dataset_id"
reference_dataset_id = gmap_option_dict.get('identification', {}).get('reference_dataset_id', not_found)
is_reference_dataset_id_OK = True
if reference_dataset_id == not_found:
error_list.append('*** ERROR: the key "reference_dataset_id" is not found in the section "identification".')
is_reference_dataset_id_OK = False
OK = False
# check section "identification" - key "reference_file"
reference_file = gmap_option_dict.get('identification', {}).get('reference_file', not_found)
is_reference_file_OK = True
if reference_file == not_found:
error_list.append('*** ERROR: the key "reference_file" is not found in the section "identification".')
is_reference_file_OK = False
OK = False
# check section "identification" - key "assembly_software"
assembly_software = gmap_option_dict.get('identification', {}).get('assembly_software', not_found)
is_assembly_software_OK = True
if assembly_software == not_found:
error_list.append('*** ERROR: the key "assembly_software" is not found in the section "identification".')
is_assembly_software_OK = False
OK = False
elif assembly_software not in [xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()]:
error_list.append('*** ERROR: the key "assembly_software" value in the section "identification" must be {0} or {1} or {2} or {3} or {4} OR {5}.'.format(xlib.get_soapdenovotrans_code(), xlib.get_transabyss_code(), xlib.get_trinity_code(), xlib.get_star_code(), xlib.get_cd_hit_est_code(), xlib.get_transcript_filter_code()))
is_assembly_software_OK = False
OK = False
# check section "identification" - key "assembly_dataset_id"
assembly_dataset_id = gmap_option_dict.get('identification', {}).get('assembly_dataset_id', not_found)
is_assembly_dataset_id_OK = True
if assembly_dataset_id == not_found:
error_list.append('*** ERROR: the key "assembly_dataset_id" is not found in the section "identification".')
is_assembly_dataset_id_OK = False
OK = False
elif not assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()) and not assembly_dataset_id.startswith(xlib.get_transabyss_code()) and not assembly_dataset_id.startswith(xlib.get_trinity_code()) and not assembly_dataset_id.startswith(xlib.get_star_code()) and not assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) and not assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
error_list.append('*** ERROR: the key "assembly_dataset_id" value is not a {0} nor {1} nor {2} nor {3} nor {4} nor {5} assembly.'.format(xlib.get_soapdenovotrans_name(), xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_code()))
is_assembly_dataset_id_OK = False
OK = False
# check section "identification" - key "assembly_type"
assembly_type = gmap_option_dict.get('identification', {}).get('assembly_type', not_found)
is_assembly_type_OK = True
if assembly_type == not_found:
error_list.append('*** ERROR: the key "assembly_type" is not found in the section "identification".')
is_assembly_type_OK = False
OK = False
elif assembly_dataset_id.startswith(xlib.get_soapdenovotrans_code()):
if assembly_type.upper() not in ['CONTIGS', 'SCAFFOLDS']:
error_list.append('*** ERROR: the key "assembly_type" must be "CONTIGS" or "SCAFFOLDS" when {0} is the assembly software.'.format(xlib.get_soapdenovotrans_name()))
is_assembly_type_OK = False
OK = False
elif assembly_dataset_id.startswith(xlib.get_transabyss_code()) or assembly_dataset_id.startswith(xlib.get_trinity_code()) or assembly_dataset_id.startswith(xlib.get_star_code()) or assembly_dataset_id.startswith(xlib.get_cd_hit_est_code()) or assembly_dataset_id.startswith(xlib.get_transcript_filter_code()):
if assembly_type.upper() != 'NONE':
error_list.append('*** ERROR: the key "assembly_type" must be "NONE" when {0} or {1} or {2} or {3} or {4} is the assembly software.'.format(xlib.get_transabyss_name(), xlib.get_trinity_name(), xlib.get_star_name(), xlib.get_cd_hit_est_name(), xlib.get_transcript_filter_name()))
is_assembly_type_OK = False
OK = False
# check section "GMAP parameters"
if 'GMAP parameters' not in sections_list:
error_list.append('*** ERROR: the section "GMAP parameters" is not found.')
OK = False
else:
# check section "GMAP parameters" - key "threads"
threads = gmap_option_dict.get('GMAP parameters', {}).get('threads', not_found)
is_threads_OK = True
if threads == not_found:
error_list.append('*** ERROR: the key "threads" is not found in the section "GMAP parameters".')
is_threads_OK = False
OK = False
else:
try:
if int(threads) < 1:
error_list.append('*** ERROR: the key "threads" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_threads_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "threads" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_threads_OK = False
OK = False
# check section "GMAP parameters" - key "kmer"
kmer = gmap_option_dict.get('GMAP parameters', {}).get('kmer', not_found)
is_kmer_OK = True
if kmer == not_found:
error_list.append('*** ERROR: the key "kmer" is not found in the section "GMAP parameters".')
is_kmer_OK = False
OK = False
else:
try:
if kmer.upper() != 'NONE' and (int(kmer) < 1 or int(kmer) > 16):
error_list.append('*** ERROR: the key "kmer" in the section "GMAP parameters" must be an integer value between 1 and 16 or NONE.')
is_kmer_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "kmer" in the section "GMAP parameters" must be an integer value between 1 and 16 or NONE.')
is_kmer_OK = False
OK = False
# check section "GMAP parameters" - key "sampling"
sampling = gmap_option_dict.get('GMAP parameters', {}).get('sampling', not_found)
is_sampling_OK = True
if sampling == not_found:
error_list.append('*** ERROR: the key "sampling" is not found in the section "GMAP parameters".')
is_sampling_OK = False
OK = False
else:
try:
if sampling.upper() != 'NONE' and int(sampling) < 1:
error_list.append('*** ERROR: the key "sampling" in the section "GMAP parameters" must be an integer value greater or equal to 1 or NONE.')
is_sampling_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "sampling" in the section "GMAP parameters" must be an integer value greater or equal to 1 or NONE.')
is_sampling_OK = False
OK = False
# check section "GMAP parameters" - key "input-buffer-size"
input_buffer_size = gmap_option_dict.get('GMAP parameters', {}).get('input-buffer-size', not_found)
is_input_buffer_size_OK = True
if input_buffer_size == not_found:
error_list.append('*** ERROR: the key "input-buffer-size" is not found in the section "GMAP parameters".')
is_input_buffer_size_OK = False
OK = False
else:
try:
if int(input_buffer_size) < 1:
error_list.append('*** ERROR: the key "input-buffer-size" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_input_buffer_size_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "input-buffer-size" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_input_buffer_size_OK = False
OK = False
# check section "GMAP parameters" - key "output-buffer-size"
output_buffer_size = gmap_option_dict.get('GMAP parameters', {}).get('output-buffer-size', not_found)
is_output_buffer_size_OK = True
if output_buffer_size == not_found:
error_list.append('*** ERROR: the key "output-buffer-size" is not found in the section "GMAP parameters".')
is_output_buffer_size_OK = False
OK = False
else:
try:
if int(output_buffer_size) < 1:
error_list.append('*** ERROR: the key "output-buffer-size" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_output_buffer_size_OK = False
OK = False
except:
error_list.append('*** ERROR: the key "output-buffer-size" in the section "GMAP parameters" must be an integer value greater or equal to 1.')
is_output_buffer_size_OK = False
OK = False
# check section "GMAP parameters" - key "prunelevel"
prunelevel = gmap_option_dict.get('GMAP parameters', {}).get('prunelevel', not_found)
is_prunelevel_OK = True
if prunelevel == not_found:
error_list.append('*** ERROR: the key "prunelevel" is not found in the section "GMAP parameters".')
is_prunelevel_OK = False
OK = False
else:
if prunelevel not in ['0', '1', '2', '3']:
error_list.append('*** ERROR: the key "prunelevel" in the section "GMAP parameters" must be 0 (no pruning) or 1 (poor seqs) or 2 (repetitive seqs) or 3 (poor and repetitive).')
is_prunelevel_OK = False
OK = False
# check section "GMAP parameters" - key "format"
format = gmap_option_dict.get('GMAP parameters', {}).get('format', not_found)
is_format_OK = True
if format == not_found:
error_list.append('*** ERROR: the key "format" is not found in the section "GMAP parameters".')
is_format_OK = False
OK = False
else:
if format.upper() not in ['COMPRESS', 'SUMMARY', 'ALIGN', 'PLS', 'GFF3_GENE', 'SPLICESITES', 'INTRONS', 'MAP_EXONS', 'MAP_RANGES', 'COORDS']:
error_list.append('*** ERROR: the key "format" in the section "GMAP parameters" must be COMPRESS or SUMMARY or ALIGN or PLS or GFF3_GENE or SPLICESITES or INTRONS or MAP_EXONS or MAP_RANGES or COORDS.')
is_format_OK = False
OK = False
# check section "GMAP parameters" - key "other_parameters"
not_allowed_parameters_list = ['nthreads', 'kmer', 'sampling', 'input-buffer-size', 'output-buffer-size', 'prunelevel', 'compress', 'summary', 'align', 'format' ]
other_parameters = gmap_option_dict.get('GMAP parameters', {}).get('other_parameters', not_found)
is_other_parameters_OK = True
if other_parameters == not_found:
error_list.append('*** ERROR: the key "other_parameters" is not found in the section "GMAP parameters".')
is_other_parameters_OK = False
OK = False
else:
if other_parameters.upper() != 'NONE':
parameter_list = [x.strip() for x in other_parameters.split(';')]
for parameter in parameter_list:
try:
if parameter.find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter)
parameter_name = mo.group(1).strip()
except:
error_list.append('*** ERROR: the value of the key "other_parameters" in the section "GMAP parameters" must be NONE or a valid parameter list.')
is_other_parameters_OK = False
OK = False
break
else:
if parameter_name in not_allowed_parameters_list:
error_list.append('*** ERROR: the parameter {0} is not allowed in the key "other_parameters" of the section "GMAP parameters" because it is controled by NGScloud.'.format(parameter_name))
is_other_parameters_OK = False
OK = False
# warn that the results config file is not valid if there are any errors
if not OK:
error_list.append('\nThe {0} config file is not valid. Please, correct this file or recreate it.'.format(xlib.get_gmap_name()))
# return the control variable and the error list
return (OK, error_list)
def build_cd_hit_est_process_script(cluster_name, current_run_dir):
'''
Build the current CD-HIT-EST process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the option dictionary
cd_hit_est_option_dict = xlib.get_option_dict(get_cd_hit_est_config_file())
# get the options
experiment_id = cd_hit_est_option_dict['identification']['experiment_id']
assembly_software = cd_hit_est_option_dict['identification'][
'assembly_software']
assembly_dataset_id = cd_hit_est_option_dict['identification'][
'assembly_dataset_id']
assembly_type = cd_hit_est_option_dict['identification']['assembly_type']
threads = cd_hit_est_option_dict['CD-HIT-EST parameters']['threads']
memory_limit = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'memory_limit']
seq_identity_threshold = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'seq_identity_threshold']
word_length = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'word_length']
mask = cd_hit_est_option_dict['CD-HIT-EST parameters']['mask']
match = cd_hit_est_option_dict['CD-HIT-EST parameters']['match']
mismatch = cd_hit_est_option_dict['CD-HIT-EST parameters']['mismatch']
other_parameters = cd_hit_est_option_dict['CD-HIT-EST parameters'][
'other_parameters']
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type == 'CONTIGS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.contig'
elif assembly_type == 'SCAFFOLDS':
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/{experiment_id}-{assembly_dataset_id}.scafSeq'
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/transabyss-final.fa'
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity.fasta'
elif assembly_software == xlib.get_ggtrinity_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/Trinity-GG.fasta'
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/clustered-transcriptome.fasta'
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = f'{xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id)}/filtered-transcriptome.fasta'
# set the output file path
if OK:
output_file = f'{current_run_dir}/clustered-transcriptome.fasta'
# write the CD-HIT-EST process script
try:
if not os.path.exists(os.path.dirname(
get_cd_hit_est_process_script())):
os.makedirs(os.path.dirname(get_cd_hit_est_process_script()))
with open(get_cd_hit_est_process_script(),
mode='w',
encoding='iso-8859-1',
newline='\n') as script_file_id:
script_file_id.write('#!/bin/bash\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
'SEP="#########################################"\n')
script_file_id.write(
'export HOST_IP=`curl --silent checkip.amazonaws.com`\n')
script_file_id.write(
'export HOST_ADDRESS="ec2-${HOST_IP//./-}-compute-1.amazonaws.com"\n'
)
script_file_id.write(
'export AWS_CONFIG_FILE=/home/ubuntu/.aws/config\n')
script_file_id.write(
'export AWS_SHARED_CREDENTIALS_FILE=/home/ubuntu/.aws/credentials\n'
)
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
f'MINICONDA3_BIN_PATH={xlib.get_cluster_app_dir()}/{xlib.get_miniconda3_name()}/bin\n'
)
script_file_id.write(f'export PATH=$MINICONDA3_BIN_PATH:$PATH\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(
f'STATUS_DIR={xlib.get_status_dir(current_run_dir)}\n')
script_file_id.write(
f'SCRIPT_STATUS_OK={xlib.get_status_ok(current_run_dir)}\n')
script_file_id.write(
f'SCRIPT_STATUS_WRONG={xlib.get_status_wrong(current_run_dir)}\n'
)
script_file_id.write('mkdir --parents $STATUS_DIR\n')
script_file_id.write(
'if [ -f $SCRIPT_STATUS_OK ]; then rm $SCRIPT_STATUS_OK; fi\n')
script_file_id.write(
'if [ -f $SCRIPT_STATUS_WRONG ]; then rm $SCRIPT_STATUS_WRONG; fi\n'
)
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write(f'CURRENT_DIR={current_run_dir}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function init\n')
script_file_id.write('{\n')
script_file_id.write(' INIT_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(
' echo "Script started at $FORMATTED_INIT_DATETIME+00:00."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(f' echo "CLUSTER: {cluster_name}"\n')
script_file_id.write(' echo "HOST NAME: $HOSTNAME"\n')
script_file_id.write(' echo "HOST IP: $HOST_IP"\n')
script_file_id.write(' echo "HOST ADDRESS: $HOST_ADDRESS"\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function run_cd_hit_est_process\n')
script_file_id.write('{\n')
script_file_id.write(
f' source activate {xlib.get_cd_hit_anaconda_code()}\n')
script_file_id.write(' cd $CURRENT_DIR\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' echo "Filtering transcriptome ..."\n')
script_file_id.write(' /usr/bin/time \\\n')
script_file_id.write(
f' --format="{xlib.get_time_output_format()}" \\\n')
script_file_id.write(' cd-hit-est \\\n')
script_file_id.write(f' -T {threads} \\\n')
script_file_id.write(f' -M {memory_limit} \\\n')
script_file_id.write(f' -i {transcriptome_file} \\\n')
script_file_id.write(
f' -c {seq_identity_threshold} \\\n')
script_file_id.write(f' -n {word_length} \\\n')
script_file_id.write(f' -mask {mask} \\\n')
script_file_id.write(f' -match {match} \\\n')
script_file_id.write(f' -mismatch {mismatch} \\\n')
if other_parameters.upper() == 'NONE':
script_file_id.write(f' -o {output_file}\n')
else:
script_file_id.write(f' -o {output_file} \\\n')
parameter_list = [
x.strip() for x in other_parameters.split(';')
]
for i in range(len(parameter_list)):
if parameter_list[i].find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
if i < len(parameter_list) - 1:
script_file_id.write(
f' -{parameter_name} {parameter_value} \\\n'
)
else:
script_file_id.write(
f' -{parameter_name} {parameter_value}\n'
)
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
if i < len(parameter_list):
script_file_id.write(
f' -{parameter_name} \\\n')
else:
script_file_id.write(
f' -{parameter_name}\n')
i += 1
script_file_id.write(' RC=$?\n')
script_file_id.write(
' if [ $RC -ne 0 ]; then manage_error cd-hit-est $RC; fi\n')
script_file_id.write(' echo "The transcriptome is filtered."\n')
script_file_id.write(' conda deactivate\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function end\n')
script_file_id.write('{\n')
script_file_id.write(' END_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' calculate_duration\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(
' echo "Script ended OK at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' send_mail ok\n')
script_file_id.write(' touch $SCRIPT_STATUS_OK\n')
script_file_id.write(' exit 0\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function manage_error\n')
script_file_id.write('{\n')
script_file_id.write(' END_DATETIME=`date --utc +%s`\n')
script_file_id.write(
' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`\n'
)
script_file_id.write(' calculate_duration\n')
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' echo "ERROR: $1 returned error $2"\n')
script_file_id.write(
' echo "Script ended WRONG at $FORMATTED_END_DATETIME+00:00 with a run duration of $DURATION s ($FORMATTED_DURATION)."\n'
)
script_file_id.write(' echo "$SEP"\n')
script_file_id.write(' send_mail wrong\n')
script_file_id.write(' touch $SCRIPT_STATUS_WRONG\n')
script_file_id.write(' exit 3\n')
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
process_name = f'{xlib.get_cd_hit_est_name()} process'
mail_message_ok = xlib.get_mail_message_ok(process_name,
cluster_name)
mail_message_wrong = xlib.get_mail_message_wrong(
process_name, cluster_name)
script_file_id.write('function send_mail\n')
script_file_id.write('{\n')
script_file_id.write(
f' SUBJECT="{xlib.get_project_name()}: {process_name}"\n')
script_file_id.write(' if [ "$1" == "ok" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_ok}"\n')
script_file_id.write(' elif [ "$1" == "wrong" ]; then\n')
script_file_id.write(f' MESSAGE="{mail_message_wrong}"\n')
script_file_id.write(' else\n')
script_file_id.write(' MESSAGE=""\n')
script_file_id.write(' fi\n')
script_file_id.write(
' DESTINATION_FILE=mail-destination.json\n')
script_file_id.write(' echo "{" > $DESTINATION_FILE\n')
script_file_id.write(
f' echo " \\\"ToAddresses\\\": [\\\"{xconfiguration.get_contact_data()}\\\"]," >> $DESTINATION_FILE\n'
)
script_file_id.write(
' echo " \\\"CcAddresses\\\": []," >> $DESTINATION_FILE\n'
)
script_file_id.write(
' echo " \\\"BccAddresses\\\": []" >> $DESTINATION_FILE\n'
)
script_file_id.write(' echo "}" >> $DESTINATION_FILE\n')
script_file_id.write(' MESSAGE_FILE=mail-message.json\n')
script_file_id.write(' echo "{" > $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Subject\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Data\\\": \\\"$SUBJECT\\\"," >> $MESSAGE_FILE\n'
)
script_file_id.write(
' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n'
)
script_file_id.write(' echo " }," >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Body\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Html\\\": {" >> $MESSAGE_FILE\n')
script_file_id.write(
' echo " \\\"Data\\\": \\\"$MESSAGE\\\"," >> $MESSAGE_FILE\n'
)
script_file_id.write(
' echo " \\\"Charset\\\": \\\"UTF-8\\\"" >> $MESSAGE_FILE\n'
)
script_file_id.write(' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write(' echo " }" >> $MESSAGE_FILE\n')
script_file_id.write(' echo "}" >> $MESSAGE_FILE\n')
script_file_id.write(
f' aws ses send-email --from {xconfiguration.get_contact_data()} --destination file://$DESTINATION_FILE --message file://$MESSAGE_FILE\n'
)
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('function calculate_duration\n')
script_file_id.write('{\n')
script_file_id.write(
' DURATION=`expr $END_DATETIME - $INIT_DATETIME`\n')
script_file_id.write(' HH=`expr $DURATION / 3600`\n')
script_file_id.write(' MM=`expr $DURATION % 3600 / 60`\n')
script_file_id.write(' SS=`expr $DURATION % 60`\n')
script_file_id.write(
' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`\n'
)
script_file_id.write('}\n')
script_file_id.write(
'#-------------------------------------------------------------------------------\n'
)
script_file_id.write('init\n')
script_file_id.write('run_cd_hit_est_process\n')
script_file_id.write('end\n')
except Exception as e:
error_list.append(f'*** EXCEPTION: "{e}".')
error_list.append(
f'*** ERROR: The file {get_cd_hit_est_process_script()} can not be created'
)
OK = False
# return the control variable and the error list
return (OK, error_list)
def build_gmap_process_script(cluster_name, current_run_dir):
'''
Build the current GMAP process script.
'''
# initialize the control variable and the error list
OK = True
error_list = []
# get the GMAP option dictionary
gmap_option_dict = xlib.get_option_dict(get_gmap_config_file())
# get the options
experiment_id = gmap_option_dict['identification']['experiment_id']
reference_dataset_id = gmap_option_dict['identification']['reference_dataset_id']
reference_file = gmap_option_dict['identification']['reference_file']
assembly_software = gmap_option_dict['identification']['assembly_software']
assembly_dataset_id = gmap_option_dict['identification']['assembly_dataset_id']
assembly_type = gmap_option_dict['identification']['assembly_type']
threads = gmap_option_dict['GMAP parameters']['threads']
kmer = gmap_option_dict['GMAP parameters']['kmer']
sampling = gmap_option_dict['GMAP parameters']['sampling']
input_buffer_size = gmap_option_dict['GMAP parameters']['input-buffer-size']
output_buffer_size = gmap_option_dict['GMAP parameters']['output-buffer-size']
prunelevel = gmap_option_dict['GMAP parameters']['prunelevel']
format = gmap_option_dict['GMAP parameters']['format']
other_parameters = gmap_option_dict['GMAP parameters']['other_parameters']
# set the cluster reference dataset directory
cluster_reference_dataset_dir = xlib.get_cluster_reference_dataset_dir(reference_dataset_id)
# set the cluster reference file
cluster_reference_file = xlib.get_cluster_reference_file(reference_dataset_id, reference_file)
# set the GMAP database name
reference_file_name, reference_file_extension = os.path.splitext(reference_file)
gmap_database = '{0}-gmap_database'.format(reference_file_name)
# set the transcriptome file path
if assembly_software == xlib.get_soapdenovotrans_code():
if assembly_type.upper() == 'CONTIGS':
transcriptome_file = '{0}/{1}-{2}.contig'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_type.upper() == 'SCAFFOLDS':
transcriptome_file = '{0}/{1}-{2}.scafSeq'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id), experiment_id, assembly_dataset_id)
elif assembly_software == xlib.get_transabyss_code():
transcriptome_file = '{0}/transabyss-final.fa'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_trinity_code():
transcriptome_file = '{0}/Trinity.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_star_code():
transcriptome_file = '{0}/Trinity-GG.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_cd_hit_est_code():
transcriptome_file = '{0}/clustered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
elif assembly_software == xlib.get_transcript_filter_code():
transcriptome_file = '{0}/filtered-transcriptome.fasta'.format(xlib.get_cluster_experiment_result_dataset_dir(experiment_id, assembly_dataset_id))
# set the output file path
output_file = 'gmap_output_{0}.txt'.format(format.lower())
# get the GMAP process script name
gmap_process_script = get_gmap_process_script()
# write the GMAP process script
try:
if not os.path.exists(os.path.dirname(gmap_process_script)):
os.makedirs(os.path.dirname(gmap_process_script))
with open(gmap_process_script, mode='w', encoding='utf8', newline='\n') as file_id:
file_id.write('{0}\n'.format('#!/bin/bash'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('GMAP_GSNAP_PATH={0}/{1}/envs/{2}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name(), xlib.get_gmap_gsnap_bioconda_code())))
file_id.write('{0}\n'.format('PATH=$GMAP_GSNAP_PATH:$PATH'))
file_id.write('{0}\n'.format('SEP="#########################################"'))
file_id.write('{0}\n'.format('cd {0}/{1}/bin'.format(xlib.get_cluster_app_dir(), xlib.get_miniconda3_name())))
file_id.write('{0}\n'.format('source activate {0}'.format(xlib.get_gmap_gsnap_bioconda_code())))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function init'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' INIT_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_INIT_DATETIME=`date --date="@$INIT_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script started in node $HOSTNAME of cluster {0} at $FORMATTED_INIT_DATETIME UTC."'.format(cluster_name)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function build_gmap_database'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' /usr/bin/time \\'))
file_id.write('{0}\n'.format(' --format="$SEP\\nElapsed real time (s): %e\\nCPU time in kernel mode (s): %S\\nCPU time in user mode (s): %U\\nPercentage of CPU: %P\\nMaximum resident set size(Kb): %M\\nAverage total memory use (Kb):%K" \\'))
file_id.write('{0}\n'.format(' gmap_build \\'))
file_id.write('{0}\n'.format(' --dir={0}\\'.format(cluster_reference_dataset_dir)))
file_id.write('{0}\n'.format(' --db={0}\\'.format(gmap_database)))
if kmer.upper() != 'NONE':
file_id.write('{0}\n'.format(' --kmer={0} \\'.format(kmer)))
file_id.write('{0}\n'.format(' {0}'.format(cluster_reference_file)))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function run_gmap_process'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' cd {0}'.format(current_run_dir)))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' gmap --version'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' /usr/bin/time \\'))
file_id.write('{0}\n'.format(' --format="$SEP\\nElapsed real time (s): %e\\nCPU time in kernel mode (s): %S\\nCPU time in user mode (s): %U\\nPercentage of CPU: %P\\nMaximum resident set size(Kb): %M\\nAverage total memory use (Kb):%K" \\'))
file_id.write('{0}\n'.format(' gmap \\'))
file_id.write('{0}\n'.format(' --nthreads={0} \\'.format(threads)))
file_id.write('{0}\n'.format(' --dir={0} \\'.format(cluster_reference_dataset_dir)))
file_id.write('{0}\n'.format(' --db={0} \\'.format(gmap_database)))
if kmer.upper() != 'NONE':
file_id.write('{0}\n'.format(' --kmer={0} \\'.format(kmer)))
if sampling.upper() != 'NONE':
file_id.write('{0}\n'.format(' --sampling={0} \\'.format(sampling)))
file_id.write('{0}\n'.format(' --input-buffer-size={0} \\'.format(input_buffer_size)))
file_id.write('{0}\n'.format(' --output-buffer-size={0} \\'.format(output_buffer_size)))
file_id.write('{0}\n'.format(' --prunelevel={0} \\'.format(prunelevel)))
if format.upper() == 'COMPRESS':
file_id.write('{0}\n'.format(' --compress \\'))
elif format.upper() == 'SUMMARY':
file_id.write('{0}\n'.format(' --summary \\'))
elif format.upper() == 'ALIGN':
file_id.write('{0}\n'.format(' --align \\'))
else:
file_id.write('{0}\n'.format(' --format={0} \\'.format(format.lower())))
file_id.write('{0}\n'.format(' --ordered \\'))
file_id.write('{0}\n'.format(' --nofails \\'))
if other_parameters.upper() != 'NONE':
parameter_list = [x.strip() for x in other_parameters.split(';')]
for i in range(len(parameter_list)):
if parameter_list[i].find('=') > 0:
pattern = r'^--(.+)=(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
parameter_value = mo.group(2).strip()
file_id.write('{0}\n'.format(' --{0}={1} \\'.format(parameter_name, parameter_value)))
else:
pattern = r'^--(.+)$'
mo = re.search(pattern, parameter_list[i])
parameter_name = mo.group(1).strip()
file_id.write('{0}\n'.format(' --{0} \\'.format(parameter_name)))
file_id.write('{0}\n'.format(' {0} \\'.format(transcriptome_file)))
file_id.write('{0}\n'.format(' > {0}'.format(output_file)))
file_id.write('{0}\n'.format(' RC=$?'))
file_id.write('{0}\n'.format(' if [ $RC -ne 0 ]; then manage_error gmap $RC; fi'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function end'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "Script ended OK at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_gmap_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended OK at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_gmap_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 0'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function manage_error'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' END_DATETIME=`date --utc +%s`'))
file_id.write('{0}\n'.format(' FORMATTED_END_DATETIME=`date --date="@$END_DATETIME" "+%Y-%m-%d %H:%M:%S"`'))
file_id.write('{0}\n'.format(' calculate_duration'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' echo "ERROR: $1 returned error $2"'))
file_id.write('{0}\n'.format(' echo "Script ended WRONG at $FORMATTED_END_DATETIME UTC with a run duration of $DURATION s ($FORMATTED_DURATION)."'))
file_id.write('{0}\n'.format(' echo "$SEP"'))
file_id.write('{0}\n'.format(' RECIPIENT={0}'.format(xconfiguration.get_contact_data())))
file_id.write('{0}\n'.format(' SUBJECT="{0}: {1} process"'.format(xlib.get_project_name(), xlib.get_gmap_name())))
file_id.write('{0}\n'.format(' MESSAGE="The {0} process in node $HOSTNAME of cluster {1} ended WRONG at $FORMATTED_END_DATETIME with a run duration of $DURATION s ($FORMATTED_DURATION). Please review its log.<br/><br/>Regards,<br/>GI Genetica, Fisiologia e Historia Forestal<br/>Dpto. Sistemas y Recursos Naturales<br/>ETSI Montes, Forestal y del Medio Natural<br/>Universidad Politecnica de Madrid<br/>https://github.com/ggfhf/"'.format(xlib.get_gmap_name(), cluster_name)))
file_id.write('{0}\n'.format(' mail --append "Content-type: text/html;" --subject "$SUBJECT" "$RECIPIENT" <<< "$MESSAGE"'))
file_id.write('{0}\n'.format(' exit 3'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('function calculate_duration'))
file_id.write('{0}\n'.format('{'))
file_id.write('{0}\n'.format(' DURATION=`expr $END_DATETIME - $INIT_DATETIME`'))
file_id.write('{0}\n'.format(' HH=`expr $DURATION / 3600`'))
file_id.write('{0}\n'.format(' MM=`expr $DURATION % 3600 / 60`'))
file_id.write('{0}\n'.format(' SS=`expr $DURATION % 60`'))
file_id.write('{0}\n'.format(' FORMATTED_DURATION=`printf "%03d:%02d:%02d\\n" $HH $MM $SS`'))
file_id.write('{0}\n'.format('}'))
file_id.write('{0}\n'.format('#-------------------------------------------------------------------------------'))
file_id.write('{0}\n'.format('init'))
file_id.write('{0}\n'.format('build_gmap_database'))
file_id.write('{0}\n'.format('run_gmap_process'))
file_id.write('{0}\n'.format('end'))
except:
error_list.append('*** ERROR: The file {0} can not be created'.format(gmap_process_script))
OK = False
# return the control variable and the error list
return (OK, error_list)
def form_list_cluster_experiment_processes():
'''
List the processes of an experiment in the cluster.
'''
# initialize the control variable
OK = True
# print the header
clib.clear_screen()
clib.print_headers_with_environment(
'Logs - List experiment processes in the cluster')
# get the cluster name
print(xlib.get_separator())
if xec2.get_running_cluster_list(only_environment_cluster=True,
volume_creator_included=False) != []:
cluster_name = cinputs.input_cluster_name(
volume_creator_included=False, help=True)
else:
print('WARNING: There is not any running cluster.')
OK = False
# create the SSH client connection
if OK:
(OK, error_list,
ssh_client) = xssh.create_ssh_client_connection(cluster_name)
for error in error_list:
print(error)
# get experiment identification
if OK:
experiment_id = cinputs.input_experiment_id(ssh_client, help=True)
if experiment_id == '':
print(
f'WARNING: The cluster {cluster_name} does not have experiment data.'
)
OK = False
# get the result dataset list of the experiment
if OK:
command = f'cd {xlib.get_cluster_result_dir()}/{experiment_id}; for list in `ls`; do ls -ld $list | grep -v ^- > /dev/null && echo $list; done;'
(OK, stdout, _) = xssh.execute_cluster_command(ssh_client, command)
if OK:
result_dataset_id_list = []
for line in stdout:
line = line.rstrip('\n')
if line != 'lost+found':
result_dataset_id_list.append(line)
# print the result dataset identification list of the experiment
if OK:
print(xlib.get_separator())
if result_dataset_id_list == []:
print(
f'*** WARNING: There is not any result dataset of the experiment {experiment_id}.'
)
else:
result_dataset_id_list.sort()
# set data width
result_dataset_width = 30
bioinfo_app_width = 25
# set line
line = '{0:' + str(result_dataset_width) + '} {1:' + str(
bioinfo_app_width) + '}'
# print header
print(line.format('Result dataset', 'Bioinfo app / Utility'))
print(
line.format('=' * result_dataset_width,
'=' * bioinfo_app_width))
# print detail lines
for result_dataset_id in result_dataset_id_list:
if result_dataset_id.startswith(xlib.get_bedtools_code() +
'-'):
bioinfo_app_name = xlib.get_bedtools_name()
elif result_dataset_id.startswith(xlib.get_blastplus_code() +
'-'):
bioinfo_app_name = xlib.get_blastplus_name()
elif result_dataset_id.startswith(xlib.get_bcftools_code() +
'-'):
bioinfo_app_name = xlib.get_bcftools_name()
elif result_dataset_id.startswith(xlib.get_bowtie2_code() +
'-'):
bioinfo_app_name = xlib.get_bowtie2_name()
elif result_dataset_id.startswith(xlib.get_busco_code() + '-'):
bioinfo_app_name = xlib.get_busco_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_code() +
'-'):
bioinfo_app_name = xlib.get_cd_hit_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_est_code() +
'-'):
bioinfo_app_name = xlib.get_cd_hit_est_name()
elif result_dataset_id.startswith(xlib.get_cuffdiff_code() +
'-'):
bioinfo_app_name = xlib.get_cuffdiff_name()
elif result_dataset_id.startswith(xlib.get_cufflinks_code() +
'-'):
bioinfo_app_name = xlib.get_cufflinks_name()
elif result_dataset_id.startswith(
xlib.get_cufflinks_cuffmerge_code() + '-'):
bioinfo_app_name = xlib.get_cufflinks_cuffmerge_name()
elif result_dataset_id.startswith(xlib.get_cuffnorm_code() +
'-'):
bioinfo_app_name = xlib.get_cuffnorm_name()
elif result_dataset_id.startswith(xlib.get_cuffquant_code() +
'-'):
bioinfo_app_name = xlib.get_cuffquant_name()
elif result_dataset_id.startswith(xlib.get_cutadapt_code() +
'-'):
bioinfo_app_name = xlib.get_cutadapt_name()
elif result_dataset_id.startswith(
xlib.get_ddradseq_simulation_code() + '-'):
bioinfo_app_name = xlib.get_ddradseq_simulation_name()
elif result_dataset_id.startswith(
xlib.get_ddradseqtools_code() + '-'):
bioinfo_app_name = xlib.get_ddradseqtools_name()
elif result_dataset_id.startswith(xlib.get_detonate_code() +
'-'):
bioinfo_app_name = xlib.get_detonate_name()
elif result_dataset_id.startswith(xlib.get_diamond_code() +
'-'):
bioinfo_app_name = xlib.get_diamond_name()
elif result_dataset_id.startswith(xlib.get_emboss_code() +
'-'):
bioinfo_app_name = xlib.get_emboss_name()
elif result_dataset_id.startswith(
xlib.get_entrez_direct_code() + '-'):
bioinfo_app_name = xlib.get_entrez_direct_name()
elif result_dataset_id.startswith(xlib.get_express_code() +
'-'):
bioinfo_app_name = xlib.get_express_name()
elif result_dataset_id.startswith(xlib.get_fastqc_code() +
'-'):
bioinfo_app_name = xlib.get_fastqc_name()
elif result_dataset_id.startswith(xlib.get_ggtrinity_code() +
'-'):
bioinfo_app_name = xlib.get_ggtrinity_name()
elif result_dataset_id.startswith(xlib.get_gmap_gsnap_code() +
'-'):
bioinfo_app_name = xlib.get_gmap_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gmap_code() + '-'):
bioinfo_app_name = xlib.get_gmap_name()
elif result_dataset_id.startswith(xlib.get_gsnap_code() + '-'):
bioinfo_app_name = xlib.get_gsnap_name()
elif result_dataset_id.startswith(xlib.get_gzip_code() + '-'):
bioinfo_app_name = xlib.get_gzip_name()
elif result_dataset_id.startswith(xlib.get_hisat2_code() +
'-'):
bioinfo_app_name = xlib.get_hisat2_name()
elif result_dataset_id.startswith(xlib.get_htseq_code() + '-'):
bioinfo_app_name = xlib.get_htseq_name()
elif result_dataset_id.startswith(xlib.get_htseq_count_code() +
'-'):
bioinfo_app_name = xlib.get_htseq_count_name()
elif result_dataset_id.startswith(
xlib.get_insilico_read_normalization_code() + '-'):
bioinfo_app_name = xlib.get_insilico_read_normalization_name(
)
elif result_dataset_id.startswith(xlib.get_ipyrad_code() +
'-'):
bioinfo_app_name = xlib.get_ipyrad_name()
elif result_dataset_id.startswith(xlib.get_kallisto_code() +
'-'):
bioinfo_app_name = xlib.get_kallisto_name()
elif result_dataset_id.startswith(xlib.get_miniconda3_code() +
'-'):
bioinfo_app_name = xlib.get_miniconda3_name()
elif result_dataset_id.startswith(xlib.get_ngshelper_code() +
'-'):
bioinfo_app_name = xlib.get_ngshelper_name()
elif result_dataset_id.startswith(xlib.get_quast_code() + '-'):
bioinfo_app_name = xlib.get_quast_name()
elif result_dataset_id.startswith(xlib.get_r_code() + '-'):
bioinfo_app_name = xlib.get_r_name()
elif result_dataset_id.startswith(xlib.get_raddesigner_code() +
'-'):
bioinfo_app_name = xlib.get_raddesigner_name()
elif result_dataset_id.startswith(xlib.get_ref_eval_code() +
'-'):
bioinfo_app_name = xlib.get_ref_eval_name()
elif result_dataset_id.startswith(xlib.get_rnaquast_code() +
'-'):
bioinfo_app_name = xlib.get_rnaquast_name()
elif result_dataset_id.startswith(xlib.get_rsem_code() + '-'):
bioinfo_app_name = xlib.get_rsem_name()
elif result_dataset_id.startswith(xlib.get_rsem_eval_code() +
'-'):
bioinfo_app_name = xlib.get_rsem_eval_name()
elif result_dataset_id.startswith(xlib.get_rsitesearch_code() +
'-'):
bioinfo_app_name = xlib.get_rsitesearch_name()
elif result_dataset_id.startswith(xlib.get_samtools_code() +
'-'):
bioinfo_app_name = xlib.get_samtools_name()
elif result_dataset_id.startswith(xlib.get_soapdenovo2_code() +
'-'):
bioinfo_app_name = xlib.get_soapdenovo2_name()
elif result_dataset_id.startswith(
xlib.get_soapdenovotrans_code() + '-'):
bioinfo_app_name = xlib.get_soapdenovotrans_name()
elif result_dataset_id.startswith(xlib.get_star_code() + '-'):
bioinfo_app_name = xlib.get_star_name()
elif result_dataset_id.startswith(xlib.get_starcode_code() +
'-'):
bioinfo_app_name = xlib.get_starcode_name()
elif result_dataset_id.startswith(xlib.get_toa_code() + '-'):
bioinfo_app_name = xlib.get_toa_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gene_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_download_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_download_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_download_taxonomy_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_download_taxonomy_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_nucleotide_gi_code(
) + '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_nucleotide_gi_name(
)
elif result_dataset_id.startswith(
xlib.
get_toa_process_gilist_viridiplantae_protein_gi_code()
+ '-'):
bioinfo_app_name = xlib.get_toa_process_gilist_viridiplantae_protein_gi_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_basic_data_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_basic_data_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gene_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gene_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_go_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_go_name()
elif result_dataset_id.startswith(
xlib.get_toa_process_load_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_interpro_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_interpro_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_load_monocots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_load_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_merge_annotations_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_merge_annotations_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nr_diamond_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nr_diamond_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_nt_blastplus_db_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_nt_blastplus_db_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_aminoacid_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_aminoacid_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_pipeline_nucleotide_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_pipeline_nucleotide_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_dicots_04_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_dicots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_gymno_01_code() + '-'):
bioinfo_app_name = xlib.get_toa_process_proteome_gymno_01_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_monocots_04_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_monocots_04_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_proteome_refseq_plant_code() +
'-'):
bioinfo_app_name = xlib.get_toa_process_proteome_refseq_plant_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_rebuild_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_rebuild_toa_database_name(
)
elif result_dataset_id.startswith(
xlib.get_toa_process_recreate_toa_database_code() +
'-'):
bioinfo_app_name = xlib.get_get_toa_process_recreate_toa_database_name(
)
elif result_dataset_id.startswith(xlib.get_tophat_code() +
'-'):
bioinfo_app_name = xlib.get_tophat_name()
elif result_dataset_id.startswith(xlib.get_transabyss_code() +
'-'):
bioinfo_app_name = xlib.get_transabyss_name()
elif result_dataset_id.startswith(
xlib.get_transcript_filter_code() + '-'):
bioinfo_app_name = xlib.get_transcript_filter_name()
elif result_dataset_id.startswith(
xlib.get_transcriptome_blastx_code() + '-'):
bioinfo_app_name = xlib.get_transcriptome_blastx_name()
elif result_dataset_id.startswith(
xlib.get_transdecoder_code() + '-'):
bioinfo_app_name = xlib.get_transdecoder_name()
elif result_dataset_id.startswith(xlib.get_transrate_code() +
'-'):
bioinfo_app_name = xlib.get_transrate_name()
elif result_dataset_id.startswith(xlib.get_trimmomatic_code() +
'-'):
bioinfo_app_name = xlib.get_trimmomatic_name()
elif result_dataset_id.startswith(xlib.get_trinity_code() +
'-'):
bioinfo_app_name = xlib.get_trinity_name()
elif result_dataset_id.startswith(
xlib.get_variant_calling_code() + '-'):
bioinfo_app_name = xlib.get_variant_calling_name()
elif result_dataset_id.startswith(xlib.get_vcftools_code() +
'-'):
bioinfo_app_name = xlib.get_vcftools_name()
elif result_dataset_id.startswith(
xlib.get_vcftools_perl_libraries_code() + '-'):
bioinfo_app_name = xlib.get_vcftools_perl_libraries_name()
elif result_dataset_id.startswith(xlib.get_vsearch_code() +
'-'):
bioinfo_app_name = xlib.get_vsearch_name()
else:
bioinfo_app_name = 'xxx'
print(line.format(result_dataset_id, bioinfo_app_name))
# close the SSH client connection
if OK:
xssh.close_ssh_client_connection(ssh_client)
# show continuation message
print(xlib.get_separator())
input('Press [Intro] to continue ...')
