Mercurial > repos > dfornika > screen_abricate_report

annotate screen_abricate_report.py @ 1:40003338a8e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
author dfornika
date Fri, 27 Sep 2019 13:31:43 -0400
parents 2ffd23634c1e
children 1c1c680c70a0
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
1 #!/usr/bin/env python
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
2
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
3 from __future__ import print_function
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
4
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
5 import argparse
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
6 import os
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
7 import re
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
8 import sys
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
9 import csv
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
10 from pprint import pprint
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
11
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
12 def parse_screen_file(screen_file):
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
13 screen = []
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
14 with open(screen_file) as f:
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
15 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
16 for row in reader:
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
17 screen.append(row)
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
18 return screen
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
19
1
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
20 def get_fieldnames(input_file):
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
21 with open(input_file) as f:
0
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
22 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
23 row = next(reader)
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
24 fieldnames = row.keys()
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
25 return fieldnames
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
26
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
27 def main(args):
1
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
28 screen = parse_screen_file(args.screening_file)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
29 abricate_report_fieldnames = get_fieldnames(args.abricate_report)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
30 gene_detection_status_fieldnames = ['gene_name', 'detected']
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
31 with open(args.abricate_report, 'r') as f1, open(args.screened_report, 'w') as f2, open(args.gene_detection_status, 'w') as f3:
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
32 abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
33 screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"', fieldnames=abricate_report_fieldnames)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
34 gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"', fieldnames=gene_detection_status_fieldnames)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
35 screened_report_writer.writeheader()
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
36 gene_detection_status_writer.writeheader()
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
37
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
38 for gene in screen:
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
39 gene_detection_status = {
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
40 'gene_name': gene['gene_name'],
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
41 'detected': False
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
42 }
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
43 for abricate_report_row in abricate_report_reader:
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
44 if re.search(gene['regex'], abricate_report_row['GENE']):
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
45 gene_detection_status['detected'] = True
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
46 screened_report_writer.writerow(abricate_report_row)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
47 gene_detection_status_writer.writerow(gene_detection_status)
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
48 f1.seek(0) # return file pointer to start of abricate report
0
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
49
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
50
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
51 if __name__ == '__main__':
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
52 parser = argparse.ArgumentParser()
1
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
53 parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)")
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
54 parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)")
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
55 parser.add_argument("--screened_report", help="Output: Screened abricate report including only genes of interest (tsv)")
40003338a8e8 planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents: 0
diff changeset
56 parser.add_argument("--gene_detection_status", help="Output: detection status for all genes listed in the screening file (tsv)")
0
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
57 args = parser.parse_args()
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
dfornika
parents:
diff changeset
58 main(args)