diff galaxy-tools/biobank/utils/format_vessels_by_individual_output.py @ 3:43be74e62bfe draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/format_vessels_by_individual_output.py	Thu Sep 22 08:57:04 2016 -0400
@@ -0,0 +1,91 @@
+# This tool format output files from kb_query vessels_by_individual
+# into a tabular format with all data related to an individual grouped
+# in each row. The tool needs as input a mapping file like
+#
+#  individual_id   label
+#  V12311          A_STUDY:A_CODE
+#  V135115         A_STUDY:B_CODE
+#
+# in order to use a known label and not VIDs for each row
+
+import csv, sys, argparse, logging
+
+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='format kb_query vessels_by_individual output file to tabular format')
+    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', type=str, required=True,
+                        help='input file (obtained using kb_query vessels by individual tool)')
+    parser.add_argument('--map_file', type=str, required=True,
+                        help='mapping file')
+    parser.add_argument('--out_file', type=str, required=True,
+                        help='output file')
+    return parser
+
+def get_mapping(records, grouper_field, grouped_field):
+    mapping = {}
+    for rec in records:
+        mapping.setdefault(rec[grouper_field], []).append(rec[grouped_field])
+    return mapping
+
+def get_labels_mapping(reader, logger):
+    rows = [r for r in reader]
+    lmap = get_mapping(rows, 'individual', 'label')
+    logger.info('%d labels grouped for %d individuals' % (len(rows),
+                                                          len(lmap)))
+    return lmap
+
+def get_vessels_mapping(reader, logger):
+    rows = [r for r in reader]
+    vmap = get_mapping(rows, 'individual', 'vessel_label')
+    logger.info('%d vessels grouped for %d individuals' % (len(rows),
+                                                           len(vmap)))
+    return vmap
+
+def build_record(label, vessels):
+    record = {'individual_label' : '--'.join(label)}
+    for v in vessels:
+        record['vessel_%d' % (vessels.index(v) + 1)] = v
+    return record
+
+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()
+
+    with open(args.map_file) as mf:
+        reader = csv.DictReader(mf, delimiter='\t')
+        labels_map = get_labels_mapping(reader, logger)
+
+    with open(args.in_file) as inf:
+        reader = csv.DictReader(inf, delimiter='\t')
+        vessels_map = get_vessels_mapping(reader, logger)
+
+    max_vessels_count = max([len(v) for v in vessels_map.values()])
+    csv_fields = ['individual_label']
+    for x in xrange(max_vessels_count):
+        csv_fields.append('vessel_%d' % (x+1))
+
+    with open(args.out_file, 'w') as ofile:
+        writer = csv.DictWriter(ofile, csv_fields, delimiter='\t')
+        writer.writeheader()
+        for ind, vessels in vessels_map.iteritems():
+            writer.writerow(build_record(labels_map[ind], vessels))
+
+    logger.info('Job completed')
+
+if __name__ == '__main__':
+    main(sys.argv[1:])