Mercurial > repos > public-health-bioinformatics > screen_abricate_report
comparison screen_abricate_report.py @ 1:45542cd244ad draft default tip
"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 |
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| 0:2c6153023368 | 1:45542cd244ad |
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| 28 screen = parse_screen_file(args.screening_file) | 28 screen = parse_screen_file(args.screening_file) |
| 29 abricate_report_fieldnames = get_fieldnames(args.abricate_report) | 29 abricate_report_fieldnames = get_fieldnames(args.abricate_report) |
| 30 gene_detection_status_fieldnames = ['gene_name', 'detected'] | 30 gene_detection_status_fieldnames = ['gene_name', 'detected'] |
| 31 with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3: | 31 with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3: |
| 32 abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"') | 32 abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"') |
| 33 screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames) | 33 screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_reader.fieldnames) |
| 34 gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames) | 34 gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames) |
| 35 screened_report_writer.writeheader() | 35 screened_report_writer.writeheader() |
| 36 gene_detection_status_writer.writeheader() | 36 gene_detection_status_writer.writeheader() |
| 37 | 37 |
| 38 for gene in screen: | 38 for gene in screen: |