added 'sample_id' to headers for 'final_plasmid.tsv' and 'custom_plas…

…mid.txt' output files (#50)
Public-Health-Bioinformatics · May 16, 2019 · 6277800 · 6277800
1 parent 8ed390d
commit 6277800
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/cpo_pipeline/plasmids/pipeline.py b/cpo_pipeline/plasmids/pipeline.py
@@ -360,6 +360,7 @@ def main(args):
 
     with open(plasmid_output_final, 'w+') as f:
         fieldnames = [
+            'sample_id',
             'accession',
             'circularity',
             'plasmid_length',
@@ -369,14 +370,17 @@ def main(args):
             'allele',
             'incompatibility_group'
         ]
+
         writer = csv.DictWriter(f, fieldnames=fieldnames, delimiter='\t', extrasaction='ignore')
+        writer.writeheader()
         if custom_best_candidate:
             f.write(args.sample_id + '\t')
             # Truncate floats to 4 digits
             writer.writerow({k:round(v,4) if isinstance(v,float) else v for k,v in custom_best_candidate.items()})
 
     with open(plasmid_output_summary, 'w+') as f:
         fieldnames = [
+        'sample_id',
             'accession',
             'circularity',
             'plasmid_length',
@@ -387,6 +391,7 @@ def main(args):
             'incompatibility_group'
         ]
         writer = csv.DictWriter(f, fieldnames=fieldnames, delimiter='\t', extrasaction='ignore')
+        writer.writeheader()
         for candidate in custom_candidates:
             f.write(args.sample_id + '\t')
             # Truncate floats to 4 digits