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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-tools/biobank/utils/before_prepare_seq_dsample_inputs.py	Thu Sep 22 08:57:04 2016 -0400
@@ -0,0 +1,89 @@
+"""
+This tool produce files used as input by 'prepare_seq_dsample_inputs'.
+
+It needs as input an Illumina samplesheet and produce as output:
+the same samplesheet with a new column 'sample_project'
+a configuration file
+The configuration file is a YAML file with the following structure:
+
+ config_parameters:
+   study_label: study_label
+
+where study_label is mandatory
+"""
+
+import csv, sys, argparse, logging, yaml
+
+
+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='prepare inputs for VLUTIL.prepare_seq_dsample_inputs')
+    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('--samplesheet-output-file', type=str,
+                        help='output file containing flowcell samplesheet',
+                        default='./samplesheet.tsv')
+    parser.add_argument('--config-output-file', type=str,
+                        help='output file containing config definitions',
+                        default='./config_parameters.yaml')
+    parser.add_argument('--study', type=str, required=True,
+                        help='study label parameter for YAML file')
+    return parser
+
+
+def read_samplesheet(in_file):
+    with open(in_file, 'rU') as f:       
+        reader = csv.DictReader(f, delimiter='\t')
+        recs = [r for r in reader]
+        fieldnames = reader.fieldnames
+    return recs, fieldnames
+
+
+def write_samplesheet_extended(recs, fields, out_file, sample_project_label):
+    with open(out_file, 'wb') as f:
+        fields.append('SampleProject')
+        writer = csv.DictWriter(f, fields, delimiter='\t')
+        writer.writeheader()
+        for row in recs:
+            row['SampleProject'] = sample_project_label
+            writer.writerow(row)     
+
+
+def write_yaml_config_file(out_file, study_label):
+        config_data = {'config_parameters': {'study_label': study_label}}
+        with open(out_file, 'w') as f:
+            yaml.dump(config_data, f)
+
+
+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('before_prepare_seq_dsample_inputs')
+
+    logger.info('Loading data from file %s' % args.in_file)    
+    recs, out_file_header = read_samplesheet(args.in_file)
+    logger.debug('Retrieved %d records', len(recs))
+    
+    logger.info('Writing file %s' % args.samplesheet_output_file)
+    write_samplesheet_extended(recs, out_file_header, args.samplesheet_output_file,
+                               args.study)
+
+    logger.info('Writing file %s' % args.config_output_file)
+    write_yaml_config_file(args.config_output_file, args.study)
+
+if __name__ == '__main__':
+    main(sys.argv[1:])