diff screen_abricate_report.py @ 0:2c6153023368 draft

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen_abricate_report.py	Wed Oct 30 23:01:01 2019 -0400
@@ -0,0 +1,58 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import os
+import re
+import sys
+import csv
+from pprint import pprint
+
+def parse_screen_file(screen_file):
+    screen = []
+    with open(screen_file) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
+        for row in reader:
+            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:
+        abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
+        screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_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()
+
+        for gene in screen:
+            gene_detection_status = {
+                'gene_name': gene['gene_name'],
+                'detected': False
+            }
+            for abricate_report_row in abricate_report_reader:
+                if re.search(gene['regex'], abricate_report_row['GENE']):
+                    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
+
+
+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)")
+    args = parser.parse_args()
+    main(args)