diff pick_plasmids_containing_genes.py @ 4:109b9d1e2e99 draft default tip

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit 0f3fff91eb329adf437224eb8f7449853083b01e-dirty"

--- a/pick_plasmids_containing_genes.py	Sat Nov 02 01:36:30 2019 -0400
+++ b/pick_plasmids_containing_genes.py	Thu Dec 19 21:06:14 2019 +0000
@@ -3,14 +3,12 @@
 from __future__ import print_function
 
 import argparse
+import csv
 import errno
-import csv
 import os
 import re
 import shutil
-import sys
 
-from pprint import pprint
 
 def parse_screen_file(screen_file):
     screen = []
@@ -20,6 +18,7 @@
             screen.append(row)
     return screen
 
+
 def main(args):
     # create output directory
     try:
@@ -47,7 +46,7 @@
             f.seek(0)
             next(abricate_report_reader)
 
-    # copy the corresponding plasmid fasta files into outdir        
+    # copy the corresponding plasmid fasta files into outdir
     for contig in contigs_with_genes_of_interest:
         for plasmid in args.plasmids:
             copy_plasmid = False
@@ -59,6 +58,7 @@
                 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)")