--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/screen_abricate_report.py	Thu Sep 26 19:37:27 2019 -0400
@@ -0,0 +1,46 @@
+#!/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_abricate_report_fieldnames(abricate_report):
+    with open(abricate_report) 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.screen)
+    abricate_report_fieldnames = get_abricate_report_fieldnames(args.abricate_report)
+    with open(args.abricate_report) as f:
+        reader = csv.DictReader(f, delimiter="\t", quotechar='"')
+        writer = csv.DictWriter(sys.stdout, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames)
+        writer.writeheader()
+        for row in reader:
+            for gene in screen:
+                if re.search(gene['regex'], row['GENE']):
+                    writer.writerow(row)
+        
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--screen", help="TSV file defining genes to screen for")
+    parser.add_argument("abricate_report", help="Abricate output")
+    args = parser.parse_args()
+    main(args)