Mercurial > repos > dfornika > pick_plasmids_containing_genes

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

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit 0f3fff91eb329adf437224eb8f7449853083b01e-dirty"
author dfornika
date Thu, 19 Dec 2019 21:06:14 +0000
parents 2dd1a0ed7cce
children
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a938371b3bfd "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/pick_plasmids_containing_genes commit bf17791d0ee6756ebbd306614617f52034b8741c-dirty"
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import argparse
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109b9d1e2e99 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit 0f3fff91eb329adf437224eb8f7449853083b01e-dirty"
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6 import csv
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7 import errno
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8 import os
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9 import re
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10 import shutil
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a938371b3bfd "planemo upload for repository https://github.com/dfornika/galaxy/tree/master/tools/pick_plasmids_containing_genes commit bf17791d0ee6756ebbd306614617f52034b8741c-dirty"
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13 def parse_screen_file(screen_file):
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14 screen = []
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15 with open(screen_file) as f:
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16 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
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17 for row in reader:
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18 screen.append(row)
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19 return screen
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22 def main(args):
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23 # create output directory
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24 try:
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25 os.mkdir(args.outdir)
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26 except OSError as exc:
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27 if exc.errno == errno.EEXIST and os.path.isdir(args.outdir):
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28 pass
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29 else:
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30 raise
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32 # parse screening file
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33 screen = parse_screen_file(args.abricate_report_screening_file)
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34 contigs_with_genes_of_interest = []
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35 # parse all abricate reports and determine which ones contain genes of interest
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36 print("\t".join(["file", "gene_detected"]))
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38 with open(args.concatenated_abricate_reports, 'r') as f:
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39 abricate_report_reader = csv.DictReader(f, delimiter="\t", quotechar='"')
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40 for gene in screen:
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41 for abricate_report_row in abricate_report_reader:
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42 if abricate_report_row['#FILE'] == '#FILE':
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43 continue
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44 if re.search(gene['regex'], abricate_report_row['GENE']):
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45 contigs_with_genes_of_interest.append(abricate_report_row['SEQUENCE'])
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46 f.seek(0)
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47 next(abricate_report_reader)
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48
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49 # copy the corresponding plasmid fasta files into outdir
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50 for contig in contigs_with_genes_of_interest:
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51 for plasmid in args.plasmids:
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52 copy_plasmid = False
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53 with open(plasmid, 'r') as f:
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54 for line in f:
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55 if ('>' + contig) == line.rstrip():
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56 copy_plasmid = True
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57 if copy_plasmid:
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58 print("\t".join([plasmid, "True"]))
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59 shutil.copy2(plasmid, args.outdir)
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61
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62 if __name__ == '__main__':
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63 parser = argparse.ArgumentParser()
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64 parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
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65 parser.add_argument("--concatenated_abricate_reports", help="abricate reports (tsv)")
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66 parser.add_argument("--abricate_report_screening_file", help="")
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67 parser.add_argument("--outdir", dest="outdir", default=".", help="Output directory")
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68 args = parser.parse_args()
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69 main(args)