Update clinical sequecning accession file parsing function to handle …

…RSV tracking sheet format.

lib/seattleflu/id3c/cli/command/clinical.py

@@ -59,10 +59,11 @@ def clinical():
 # Parse sequencing accessions subcommand
 @clinical.command("parse-sequencing")
 @click.argument("accession_ids_filename", metavar = "<Sequencing accession IDs filename>")
+@click.argument("record_type", metavar="<record type>", type=click.Choice(['covid','rsv']))
 @click.option("-o", "--output", metavar="<output filename>",
  help="The filename for the output of missing barcodes")
 
-def parse_sequencing_accessions(accession_ids_filename, output):
+def parse_sequencing_accessions(accession_ids_filename, record_type, output):
  """
  Process sequencing accession IDs file.
 
@@ -99,10 +100,13 @@ def parse_sequencing_accessions(accession_ids_filename, output):
  'genbank_accession': 'genbank_accession',
  '_provenance': '_provenance'
  }
+ if record_type=='rsv':
+ column_map['pathogen'] = 'pathogen'
 
  clinical_records = clinical_records[(clinical_records['sfs_sample_barcode'].notnull())&(clinical_records.status=='submitted')].rename(columns=column_map)
 
- barcode_quality_control(clinical_records, output)
+ if record_type=='covid':
+ barcode_quality_control(clinical_records, output)
 
  # Drop columns we're not tracking
  clinical_records = clinical_records[column_map.values()]