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'] ))