Mercurial > repos > public-health-bioinformatics > screen_abricate_report
changeset 1:4f963b583186 draft
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
| author | public-health-bioinformatics |
|---|---|
| date | Tue, 12 Nov 2019 21:44:45 -0500 |
| parents | b2d56a44a872 |
| children | 912a3a3dc082 |
| files | screen_abricate_report.py screen_abricate_report.xml |
| diffstat | 2 files changed, 19 insertions(+), 14 deletions(-) [+] |
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--- a/screen_abricate_report.py Thu Oct 31 15:43:15 2019 -0400 +++ b/screen_abricate_report.py Tue Nov 12 21:44:45 2019 -0500 @@ -3,11 +3,9 @@ from __future__ import print_function import argparse -import os +import csv import re -import sys -import csv -from pprint import pprint + def parse_screen_file(screen_file): screen = [] @@ -17,21 +15,26 @@ screen.append(row) return screen + def get_fieldnames(input_file): with open(input_file) as f: reader = csv.DictReader(f, delimiter="\t", quotechar='"') row = next(reader) fieldnames = row.keys() return fieldnames - + + def main(args): screen = parse_screen_file(args.screening_file) - abricate_report_fieldnames = get_fieldnames(args.abricate_report) 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: + 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_reader.fieldnames) - gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_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() @@ -45,14 +48,16 @@ gene_detection_status['detected'] = True screened_report_writer.writerow(abricate_report_row) gene_detection_status_writer.writerow(gene_detection_status) - f1.seek(0) # return file pointer to start of abricate report + f1.seek(0) # return file pointer to start of abricate report if __name__ == '__main__': parser = argparse.ArgumentParser() parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)") parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)") - parser.add_argument("--screened_report", help="Output: Screened abricate report including only genes of interest (tsv)") - parser.add_argument("--gene_detection_status", help="Output: detection status for all genes listed in the screening file (tsv)") + parser.add_argument("--screened_report", help=("Output: Screened abricate report ", + "including only genes of interest (tsv)")) + parser.add_argument("--gene_detection_status", help=("Output: detection status for all genes ", + "listed in the screening file (tsv)")) args = parser.parse_args() main(args)
--- a/screen_abricate_report.xml Thu Oct 31 15:43:15 2019 -0400 +++ b/screen_abricate_report.xml Tue Nov 12 21:44:45 2019 -0500 @@ -18,8 +18,8 @@ </param> </inputs> <outputs> - <data name="screened_report" type="data" format="tabular" label="Screened Abricate Report" /> - <data name="gene_detection_status" type="data" format="tabular" label="Gene Detection Status" /> + <data name="screened_report" format="tabular" label="Screened Abricate Report" /> + <data name="gene_detection_status" format="tabular" label="Gene Detection Status" /> </outputs> <tests> <test>