Mercurial > repos > public-health-bioinformatics > screen_abricate_report

diff screen_abricate_report.py @ 1:45542cd244ad draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
author public-health-bioinformatics
date Thu, 31 Oct 2019 15:14:36 -0400
parents 2c6153023368
children
line wrap: on
line diff
--- a/screen_abricate_report.py	Wed Oct 30 23:01:01 2019 -0400
+++ b/screen_abricate_report.py	Thu Oct 31 15:14:36 2019 -0400
@@ -30,7 +30,7 @@
     gene_detection_status_fieldnames = ['gene_name', 'detected']
     with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3:
         abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
-        screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames)
+        screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_reader.fieldnames)
         gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames)
         screened_report_writer.writeheader()
         gene_detection_status_writer.writeheader()