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 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 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 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(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, 'master')
for error in error_list:
log.write('{0}\n'.format(error))
# get experiment identification
if OK:
experiment_id = cinputs.input_experiment_id(ssh_client, help=True)
if experiment_id == '':
print('WARNING: The cluster {0} has not experiment data.'.format(cluster_name))
OK = False
# get the result dataset list of the experiment
if OK:
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(), experiment_id)
(OK, stdout, stderr) = 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('*** WARNING: There is not any result dataset of the experiment {0}.'.format(experiment_id))
else:
result_dataset_id_list.sort()
# set data width
result_dataset_width = 25
bioinfo_app_width = 25
# set line template
line_template = '{0:' + str(result_dataset_width) + '} {1:' + str(bioinfo_app_width) + '}'
# print header
print(line_template.format('Result dataset', 'Bioinfo app / Utility'))
print(line_template.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_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_est_name()
elif result_dataset_id.startswith(xlib.get_cd_hit_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'
print(line_template.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 ...')
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 ...')