Mercurial > repos > dfornika > screen_abricate_report

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
author dfornika
date Thu, 02 Jan 2020 21:04:04 +0000
parents 40003338a8e8
children
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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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1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
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6 import csv
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7 import re
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10 class Range(object):
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11 """
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12 Used to limit the min_coverage and min_identity args to range 0.0 - 100.0
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13 """
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14 def __init__(self, start, end):
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15 self.start = start
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16 self.end = end
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18 def __eq__(self, other):
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19 return self.start <= other <= self.end
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21 def __contains__(self, item):
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22 return self.__eq__(item)
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24 def __iter__(self):
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25 yield self
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27 def __repr__(self):
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28 return str(self.start) + " - " + str(self.end)
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30 def parse_screen_file(screen_file):
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31 screen = []
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32 with open(screen_file) as f:
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33 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
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34 for row in reader:
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35 screen.append(row)
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36 return screen
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37
3
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38
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39 def get_fieldnames(input_file):
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40 with open(input_file) as f:
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41 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
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42 row = next(reader)
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43 fieldnames = row.keys()
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44 return fieldnames
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45
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46 def detect_gene(abricate_report_row, regex, min_coverage, min_identity):
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47 gene_of_interest = bool(re.search(regex, abricate_report_row['GENE']))
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48 sufficient_coverage = float(abricate_report_row['%COVERAGE']) >= min_coverage
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49 sufficient_identity = float(abricate_report_row['%IDENTITY']) >= min_identity
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50 if gene_of_interest and sufficient_coverage and sufficient_identity:
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51 return True
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52 else:
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53 return False
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54
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55
0
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56 def main(args):
1
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57 screen = parse_screen_file(args.screening_file)
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58 gene_detection_status_fieldnames = ['gene_name', 'detected']
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59 with open(args.abricate_report, 'r') as f1, \
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60 open(args.screened_report, 'w') as f2, \
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61 open(args.gene_detection_status, 'w') as f3:
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62 abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
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63 screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"',
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64 fieldnames=abricate_report_reader.fieldnames)
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65 gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"',
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66 fieldnames=gene_detection_status_fieldnames)
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67 screened_report_writer.writeheader()
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68 gene_detection_status_writer.writeheader()
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69
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70 for gene in screen:
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71 gene_detection_status = {
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72 'gene_name': gene['gene_name'],
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73 'detected': False
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74 }
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75 for abricate_report_row in abricate_report_reader:
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76 if detect_gene(abricate_report_row, gene['regex'], args.min_coverage, args.min_identity):
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77 gene_detection_status['detected'] = True
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78 screened_report_writer.writerow(abricate_report_row)
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79 gene_detection_status_writer.writerow(gene_detection_status)
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1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
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80 f1.seek(0) # return file pointer to start of abricate report
1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
dfornika
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81 next(abricate_report_reader)
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82
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83 if __name__ == '__main__':
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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84 parser = argparse.ArgumentParser()
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dfornika
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85 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
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86 parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)")
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1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
dfornika
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87 parser.add_argument("--screened_report", help=("Output: Screened abricate report, including only genes of interest (tsv)"))
1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
dfornika
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88 parser.add_argument("--gene_detection_status", help=("Output: detection status for all genes listed in the screening file (tsv)"))
1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
dfornika
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89 parser.add_argument("--min_coverage", type=float, default=90.0, choices=Range(0.0, 100.0), help=("Minimum percent coverage"))
1c1c680c70a0 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 2ec76aac2fcf466fc16091bfff8b7cb83fd92467-dirty"
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90 parser.add_argument("--min_identity", type=float, default=90.0, choices=Range(0.0, 100.0), help=("Minimum percent identity"))
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91 args = parser.parse_args()
2ffd23634c1e planemo upload for repository https://github.com/dfornika/galaxytools/blob/master/tools/screen_abricate_report commit d9732cd3279d03dcc498bf2eb903f9e6120a9d85-dirty
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92 main(args)