--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pick_plasmids_containing_genes.py	Tue Nov 12 22:20:54 2019 -0500
@@ -0,0 +1,69 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+
+import argparse
+import csv
+import errno
+import os
+import re
+import shutil
+
+
+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 main(args):
+    # create output directory
+    try:
+        os.mkdir(args.outdir)
+    except OSError as exc:
+        if exc.errno == errno.EEXIST and os.path.isdir(args.outdir):
+            pass
+        else:
+            raise
+
+    # parse screening file
+    screen = parse_screen_file(args.abricate_report_screening_file)
+    contigs_with_genes_of_interest = []
+    # parse all abricate reports and determine which ones contain genes of interest
+    print("\t".join(["file", "gene_detected"]))
+
+    with open(args.concatenated_abricate_reports, 'r') as f:
+        abricate_report_reader = csv.DictReader(f, delimiter="\t", quotechar='"')
+        for gene in screen:
+            for abricate_report_row in abricate_report_reader:
+                if abricate_report_row['#FILE'] == '#FILE':
+                    continue
+                if re.search(gene['regex'], abricate_report_row['GENE']):
+                    contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
+            f.seek(0)
+            next(abricate_report_reader)
+
+    # copy the corresponding plasmid fasta files into outdir
+    for contig in contigs_with_genes_of_interest:
+        for plasmid in args.plasmids:
+            copy_plasmid = False
+            with open(plasmid, 'r') as f:
+                for line in f:
+                    if ('>' + contig) == line.rstrip():
+                        copy_plasmid = True
+            if copy_plasmid:
+                print("\t".join([plasmid, "True"]))
+                shutil.copy2(plasmid, args.outdir)
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
+    parser.add_argument("--concatenated_abricate_reports", help="abricate reports (tsv)")
+    parser.add_argument("--abricate_report_screening_file", help="")
+    parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
+    args = parser.parse_args()
+    main(args)