select s.sample_name || '.' || sp.sequence_prep_id
from sample s
inner join sequence_prep sp
on s.sample_id = sp.sample_id
where s.study_id = {0}
and sp.run_prefix = '{1}'
""".format(study_id, run_prefix[:-1])
sample_and_prep = data_access.dynamicMetadataSelect(sql).fetchone()[0]
input_str = '-i {0} --sample_id {1}'.format(filenames[0], sample_and_prep)
except Exception, e:
error = 'Failed to obtain sample and sequence prep info for study_id {0} and run_prefix {1}\n'.format(study_id, run_prefix)
error += 'SQL was: \n {0} \n'.format(sql)
error += 'Original exception was: \n {0}'.format(str(e))
raise Exception(error)
else:
input_str=get_split_libraries_fastq_params_and_file_types(filenames, mapping_fp)
# create split_libaries folder
split_library_output=join(output_dir,'split_libraries')
create_dir(split_library_output)
# get params string
try:
params_str = get_params_str(params['split_libraries_fastq'])
except KeyError:
params_str = ''
# Build the split libraries command
split_libraries_cmd = '%s %s/split_libraries_fastq.py -o %s -m %s %s %s' % \
(python_exe_fp, script_dir, split_library_output, mapping_input_fp_copy,
input_str,params_str)
def run_process_illumina_through_split_lib(study_id,run_prefix,input_fp,
mapping_fp, output_dir,
command_handler, params, qiime_config,
write_to_all_fasta=False,
status_update_callback=print_to_stdout):
""" NOTE: Parts of this function are a directly copied from the
run_qiime_data_preparation function from the workflow.py library file
in QIIME.
The steps performed by this function are:
1) De-multiplex sequences. (split_libraries_fastq.py)
"""
# Prepare some variables for the later steps
filenames=input_fp.split(',')
commands = []
create_dir(output_dir)
python_exe_fp = qiime_config['python_exe_fp']
script_dir = get_qiime_scripts_dir()
logger = WorkflowLogger(generate_log_fp(output_dir),
params=params,
qiime_config=qiime_config)
# copy the mapping file
copied_mapping=split(mapping_fp)[-1]
mapping_input_fp_copy=join(output_dir, copied_mapping)
copy_mapping_cmd='cp %s %s' % (mapping_fp,mapping_input_fp_copy)
commands.append([('CopyMapping', copy_mapping_cmd)])
# sort the filenames
filenames.sort()
# determine which file is seq-file and which is barcode-file and associate
# to mapping file
input_str=get_split_libraries_fastq_params_and_file_types(filenames,
mapping_fp)
# create split_libaries folder
split_library_output=join(output_dir,'split_libraries')
create_dir(split_library_output)
# get params string
try:
params_str = get_params_str(params['split_libraries_fastq'])
except KeyError:
params_str = ''
# Build the split libraries command
split_libraries_cmd = '%s %s/split_libraries_fastq.py -o %s -m %s %s %s' % \
(python_exe_fp, script_dir, split_library_output, mapping_input_fp_copy,
input_str,params_str)
commands.append([('SplitLibraries', split_libraries_cmd)])
# define the generate files
input_fp=join(split_library_output,'seqs.fna')
# create per sample fastq files
fastq_output=join(split_library_output,'per_sample_fastq')
create_dir(fastq_output)
"""
# not used for the one-off
try:
params_str = get_params_str(params['convert_fastaqual_fastq'])
except KeyError:
params_str = ''
"""
# build the per-sample fastq command
input_qual_fp=join(split_library_output,'seqs.qual')
create_fastq_cmd = '%s %s/git/qiime_web_app/python_code/scripts/make_per_sample_fastq.py -i %s -q %s -o %s' % \
(python_exe_fp, environ['HOME'], input_fp, input_qual_fp, fastq_output)
"""
# TURN ON when convert_fastaqual_fastq can handle Illumina qual file
create_fastq_cmd = '%s %s/convert_fastaqual_fastq.py -f %s -q %s -o %s %s'%\
(python_exe_fp, script_dir, input_fp, input_qual_fp,
fastq_output, params_str)
"""
commands.append([('Create FASTQ', create_fastq_cmd)])
# Call the command handler on the list of commands
command_handler(commands,status_update_callback,logger=logger)
# Return the fasta file paths
return filenames
