Mercurial > repos > ric > test2
diff galaxy-tools/biobank/utils/prepare_seq_dsample_inputs.py @ 0:ba6cf6ede027 draft default tip
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| author | ric |
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| date | Wed, 28 Sep 2016 06:03:30 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/galaxy-tools/biobank/utils/prepare_seq_dsample_inputs.py Wed Sep 28 06:03:30 2016 -0400 @@ -0,0 +1,283 @@ +""" +This tool produces files that can be used as input to import +* samples +* flowcells +* lanes +* laneslots +within OMERO.biobank using import applications. +If the optional 'study-output-file' parameter is given as input, the +script will produce the input file for a new study definition. +If the optional 'tubes-subsamples-output-file' is given, the script +will generate another file with tubes definitions where each tube is +produced appliying a specific laboratory protocol to an existing +tube. Existing tubes are the ones in tubes-out-file, new tubes' labels +are created using the pattern <tube_label>::<protocol> +The config_parameters field must point to a YAML configuration file +with the following structure: + + config_parameters: + study_label: study_label + namespace: namespace + +where study_label is mandatory +""" + +import csv, sys, argparse, logging, yaml +# Needed to import flowcell data +from bioblend.galaxy import GalaxyInstance +import nglimsclient, os + +LOG_FORMAT = '%(asctime)s|%(levelname)-8s|%(message)s' +LOG_DATEFMT = '%Y-%m-%d %H:%M:%S' +LOG_LEVELS = ['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL'] + +def make_parser(): + parser = argparse.ArgumentParser(description='split sequencing samplesheet') + parser.add_argument('--logfile', type=str, help='log file (default=stderr)') + parser.add_argument('--loglevel', type=str, choices=LOG_LEVELS, + help='logging level', default='INFO') + parser.add_argument('--in-file', '-i', type=str, required=True, + help='input file') + parser.add_argument('--tubes-out-file', type=str, + help='output file containing tube definitions', + default='./tubes_def.tsv') + parser.add_argument('--flowcells-out-file', type=str, + help='output file containing flowcell definitions', + default='./flowcells_def.tsv') + parser.add_argument('--lanes-out-file', type=str, + help='output file containing lane definitions', + default='./lanes_def.tsv') + parser.add_argument('--laneslots-out-file', type=str, + help='output file containing laneslot definitions', + default='./laneslots_def.tsv') + parser.add_argument('--config-parameters', type=str, required=True, + help='a YAML configuration file containing study label and labels namespace, ' + 'namespace is optional') + parser.add_argument('--study-output-file', type=str, + help='output file containing study definition') + parser.add_argument('--tubes-subsamples-output-file', type=str, + help='output file containing tubes subsamples (samples produced applying a ' + 'laboratory protocol to existing samples)') + return parser + + +def get_samplesheet_translator(samplesheet_type='default'): + translator = {'default': {'flowcell_id': 'FCID', + 'tube_id': 'SampleID', + 'lane_id': 'Lane', + 'sample_tag': 'Index', + 'protocol': 'Recipe', + 'operator': 'Operator', + 'sample_project': 'SampleProject'} + } + return translator[samplesheet_type] + +def add_namespace(namespace, label, separator='|'): + return separator.join([namespace, label]) + +def write_tubes_file(records, study_label, translator, ofile, + namespace = None, logger = None): + ofile_fields = ['study', 'label', 'vessel_type', 'vessel_content', + 'vessel_status', 'source', 'source_type'] + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t') + writer.writeheader() + tubes_def = set([r[translator['tube_id'].strip()] for r in records]) + for x in tubes_def: + writer.writerow({'study' : study_label, + 'label' : x if not namespace else add_namespace(namespace, x), + 'vessel_type' : 'Tube', + 'vessel_content' : 'DNA', + 'vessel_status' : 'UNKNOWN', + 'source' : 'None', + 'source_type' : 'NO_SOURCE'}) + + +def write_subsamples_file(records, study_label, translator, ofile, + namespace = None, logger = None): + ofile_fields = ['study', 'label', 'vessel_type', 'vessel_content', + 'vessel_status', 'source', 'source_type', 'options'] + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t') + writer.writeheader() + subsamples_def = set([('%s::%s' % (r[translator['tube_id']].strip(), r[translator['protocol']].strip()), + r[translator['tube_id']].strip(), + r[translator['protocol']].strip()) for r in records]) + for x in subsamples_def: + writer.writerow({'study' : study_label, + 'label' : x[0] if not namespace else add_namespace(namespace, x[0]), + 'vessel_type' : 'Tube', + 'vessel_content' : 'DNA', + 'vessel_status' : 'UNKNOWN', + 'source' : x[1] if not namespace else add_namespace(namespace, x[1]), + 'source_type' : 'Tube', + 'options' : 'protocol=%s' % x[2]}) + + +def write_flowcells_file(records, study_label, translator, ofile, + namespace = None, logger=None): + ofile_fields = ['study', 'label', 'barcode', 'container_status', + 'number_of_slots'] + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t') + writer.writeheader() + flowcells_def = set([(r[translator['flowcell_id']].strip()) for r in records]) + for x in flowcells_def: + writer.writerow({'study' : study_label, + 'label' : x if not namespace else add_namespace(namespace, x), + 'barcode' : x if not namespace else add_namespace(namespace, x), + 'container_status' : 'INSTOCK', + 'number_of_slots' : '8'}) + + +def write_lanes_file(records, study_label, translator, ofile, + namespace = None, logger=None): + ofile_fields = ['study', 'flow_cell', 'slot', 'container_status'] + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t') + writer.writeheader() + lanes_def = set([(r[translator['flowcell_id']].strip(), + r[translator['lane_id']].strip()) + for r in records]) + for x in lanes_def: + writer.writerow({'study' : study_label, + 'flow_cell' : x[0] if not namespace else add_namespace(namespace, x[0]), + 'slot' : x[1], + 'container_status' : 'INSTOCK'}) + + +def write_laneslots_file(records, study_label, translator, ofile, + subsamples_enabled=False, + namespace = None, logger=None): + logger.debug ('subsamples_ensabled: %r' % subsamples_enabled) + ofile_fields = ['study', 'lane', 'tag', 'content', 'source', + 'source_type', 'options'] + # Get NGLIMS host and key + try: + galaxy_host = os.environ['NGLIMS_GALAXY_HOST'] + api_key = os.environ['NGLIMS_GALAXY_API_KEY'] + except KeyError as ke: + msg = 'No environment variables %s set to configure access to the Galaxy server' % ke + sys.exit(msg) + # Get flowcell label (assuming label is the same for all records) + fc_id = records[0][translator['flowcell_id']].strip() + # Get flowcell details from nglims + gi = nglimsclient.setup(GalaxyInstance(galaxy_host, api_key)) + if gi.nglims.exists_flowcell_id(fc_id): + fc_data = gi.nglims.flowcell_complete_details(fc_id) + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t') + writer.writeheader() + laneslots_def = set() + for r in records: + fc_id = r[translator['flowcell_id']].strip() if not namespace else \ + add_namespace(namespace, r[translator['flowcell_id']]).strip() + if subsamples_enabled: + source_tube_id = '%s::%s' % (r[translator['tube_id']].strip(), + r[translator['protocol']].strip()) + else: + source_tube_id = r[translator['tube_id']].strip() + # Identify adapter + adapter = [i['adapter'] for i in fc_data['details'] if i['name']==r[translator['tube_id']].strip() and i['lane']==int(r[translator['lane_id']].strip())] + laneslots_def.add(('%s:%s' % (fc_id, r[translator['lane_id']].strip()), + r[translator['sample_tag']].strip(), + source_tube_id, + r[translator['protocol']].strip(), + r[translator['operator']].strip(), + r[translator['sample_project']].strip(), + adapter[0])) + for x in laneslots_def: + writer.writerow({'study' : study_label, + 'lane' : x[0], + 'tag' : x[1], + 'content' : 'DNA', + 'source' : x[2] if not namespace else \ + add_namespace(namespace, x[2]), + 'source_type' : 'Tube', + 'options' : 'protocol=%s,operator=%s,sample_project=%s,adapter=%s' % + (x[3], x[4], x[5], x[6])}) + + +def write_study_file(study_label, records, translator, ofile, logger=None): + ofile_fields = ['label', 'description'] + with open(ofile, 'w') as out_file: + writer = csv.DictWriter(out_file, ofile_fields, delimiter='\t', ) + writer.writeheader() + writer.writerow({'label': study_label}) + + +def main(argv): + parser = make_parser() + args = parser.parse_args(argv) + + log_level = getattr(logging, args.loglevel) + kwargs = {'format' : LOG_FORMAT, + 'datefmt' : LOG_DATEFMT, + 'level' : log_level} + if args.logfile: + kwargs['filename'] = args.logfile + logging.basicConfig(**kwargs) + logger = logging.getLogger('prepare_seq_dsample_inputs') + + with open(args.in_file, 'rU') as f: + logger.info('Loading data from file %s' % args.in_file) + reader = csv.DictReader(f, delimiter='\t') + recs = [r for r in reader] + translator = get_samplesheet_translator() + + with open(args.config_parameters) as cfgf: + conf = yaml.load(cfgf) + if not conf.has_key('config_parameters'): + raise RuntimeError('Bad configuration file') + else: + try: + study_label = conf['config_parameters']['study_label'] + except KeyError: + raise RuntimeError('No study_label provided') + if conf['config_parameters'].has_key('namespace'): + namespace = conf['config_parameters']['namespace'] + else: + namespace = None + + if args.study_output_file: + logger.info('Writing Study definition file %s' % args.study_output_file) + write_study_file(study_label, recs, translator, args.study_output_file, logger) + logger.info('Done writing file %s' % args.study_output_file) + + logger.info('Writing Tube definitions file %s' % args.tubes_out_file) + write_tubes_file(recs, study_label, translator, + args.tubes_out_file, namespace, + logger) + logger.info('Done writing file %s' % args.tubes_out_file) + + if args.tubes_subsamples_output_file: + logger.info('Writing Tubes\' subsamples definitions file %s' \ + % args.tubes_subsamples_output_file) + write_subsamples_file(recs, study_label, translator, + args.tubes_subsamples_output_file, + namespace, logger) + logger.info('Done writing file %s' % args.tubes_subsamples_output_file) + + logger.info('Writing FlowCell definitions file %s' % args.flowcells_out_file) + write_flowcells_file(recs, study_label, translator, + args.flowcells_out_file, namespace, + logger) + logger.info('Done writing file %s' % args.flowcells_out_file) + + logger.info('Writing Lane definitions file %s' % args.lanes_out_file) + write_lanes_file(recs, study_label, translator, + args.lanes_out_file, namespace, + logger) + logger.info('Done writing file %s' % args.lanes_out_file) + + logger.info('Writing LaneSlot definitions file %s' % args.laneslots_out_file) + write_laneslots_file(recs, study_label, translator, + args.laneslots_out_file, + 'tubes_subsamples_output_file' in args, # Check if subsamples have been created + namespace, + logger) + logger.info('Done writing file %s' % args.laneslots_out_file) + + +if __name__ == '__main__': + main(sys.argv[1:])