def test_paired_dummy(self):
"""
Test the check_read_labels method with paired
"""
accession = {'paired': '1',
'pair_id': '1\n1',
'mate_id': '',
'label': '',
'type': ''}
check_read_labels(accession, 'dummy')
def main(workspace, accession_files):
headers = [
"project_id", "accession_id", "species", "partition", "gender", "cell",
"readType", "type", "qualities", "dataType", "rnaExtract",
"localization", "replicate", "lab"
]
template = '\t'.join(['%s'] * len(headers)) + '\n'
output_file = open(os.path.join(workspace, "accessions.csv"), "w")
output_file.write('\t'.join(headers) + '\n')
parsed_accessions = {}
for accession in accession_files:
accession_file = open(accession, 'r')
parsed_accessions[accession] = parse_accession_file(accession_file)
for key, value in parsed_accessions.items():
project_id = os.path.split(os.path.split(key)[0])[-1]
accessions = extract_accessions(value)
for accession_id, accession in accessions:
check_read_labels(accession, accession_id)
for attribute in [
'species', 'label', 'gender', 'qualities', 'replicate',
'rnaExtract', 'localization', 'cell', 'type', 'dataType',
'lab', 'readtype'
]:
if not attribute in accession:
accession[attribute] = ''
else:
if '\n' in accession[attribute]:
first = accession[attribute].split('\n')[0]
accession[attribute] = first
output_file.write(
template %
(project_id, accession_id, accession['species'],
accession['label'], accession['gender'], accession['cell'],
accession['readType'], accession['type'],
accession['qualities'], accession['dataType'],
accession['rnaExtract'], accession['localization'],
accession['replicate'], accession['lab']))
def main(workspace, accession_files):
headers = ["project_id",
"accession_id",
"species",
"partition",
"gender",
"cell",
"readType",
"type",
"qualities",
"dataType",
"rnaExtract",
"localization",
"replicate",
"lab"
]
template = '\t'.join(['%s'] * len(headers)) + '\n'
output_file = open(os.path.join(workspace, "accessions.csv"), "w")
output_file.write('\t'.join(headers) + '\n')
parsed_accessions = {}
for accession in accession_files:
accession_file = open(accession, 'r')
parsed_accessions[accession] = parse_accession_file(accession_file)
for key, value in parsed_accessions.items():
project_id = os.path.split(os.path.split(key)[0])[-1]
accessions = extract_accessions(value)
for accession_id, accession in accessions:
check_read_labels(accession, accession_id)
for attribute in ['species',
'label',
'gender',
'qualities',
'replicate',
'rnaExtract',
'localization',
'cell',
'type',
'dataType',
'lab',
'readtype']:
if not attribute in accession:
accession[attribute] = ''
else:
if '\n' in accession[attribute]:
first = accession[attribute].split('\n')[0]
accession[attribute] = first
output_file.write(template % (project_id,
accession_id,
accession['species'],
accession['label'],
accession['gender'],
accession['cell'],
accession['readType'],
accession['type'],
accession['qualities'],
accession['dataType'],
accession['rnaExtract'],
accession['localization'],
accession['replicate'],
accession['lab']
))
