Mercurial > repos > public-health-bioinformatics > screen_abricate_report

annotate screen_abricate_report.py @ 4:22247b1a59d5 draft default tip

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit ae10b1f55b2356bea735a994619288f7575430cb"
author public-health-bioinformatics
date Fri, 03 Jan 2020 14:30:22 -0500
parents 2262e531c50b
children
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
public-health-bioinformatics
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1 #!/usr/bin/env python
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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3 from __future__ import print_function
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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5 import argparse
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4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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6 import csv
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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7 import re
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4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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10 class Range(object):
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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11 """
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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12 Used to limit the min_coverage and min_identity args to range 0.0 - 100.0
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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13 """
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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14 def __init__(self, start, end):
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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15 self.start = start
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16 self.end = end
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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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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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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24 def __iter__(self):
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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25 yield self
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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27 def __repr__(self):
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28 return str(self.start) + " - " + str(self.end)
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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31 def parse_screen_file(screen_file):
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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32 screen = []
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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33 with open(screen_file) as f:
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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34 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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35 for row in reader:
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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36 screen.append(row)
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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37 return screen
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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38
1
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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40 def get_fieldnames(input_file):
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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41 with open(input_file) as f:
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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42 reader = csv.DictReader(f, delimiter="\t", quotechar='"')
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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43 row = next(reader)
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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44 fieldnames = row.keys()
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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45 return fieldnames
1
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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47
3
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48 def detect_gene(abricate_report_row, regex, min_coverage, min_identity):
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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49 gene_of_interest = bool(re.search(regex, abricate_report_row['GENE']))
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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50 sufficient_coverage = float(abricate_report_row['%COVERAGE']) >= min_coverage
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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51 sufficient_identity = float(abricate_report_row['%IDENTITY']) >= min_identity
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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52 if gene_of_interest and sufficient_coverage and sufficient_identity:
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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53 return True
2262e531c50b "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 50a464c3e6f87ca8d2c874842cbcee370d8aa9c4"
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54 else:
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55 return False
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56
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57
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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58 def main(args):
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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59 screen = parse_screen_file(args.screening_file)
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60 gene_detection_status_fieldnames = ['gene_name', 'detected', 'alleles']
1
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61 with open(args.abricate_report, 'r') as f1, \
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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62 open(args.screened_report, 'w') as f2, \
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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63 open(args.gene_detection_status, 'w') as f3:
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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64 abricate_report_reader = csv.DictReader(f1, delimiter="\t", quotechar='"')
1
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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65 screened_report_writer = csv.DictWriter(f2, delimiter="\t", quotechar='"',
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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66 fieldnames=abricate_report_reader.fieldnames)
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67 gene_detection_status_writer = csv.DictWriter(f3, delimiter="\t", quotechar='"',
4f963b583186 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit c27095ceaf23aa2c910e0ea866db9ec8d3e7816b"
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68 fieldnames=gene_detection_status_fieldnames)
0
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69 screened_report_writer.writeheader()
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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70 gene_detection_status_writer.writeheader()
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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71
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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72 for gene in screen:
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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73 gene_detection_status = {
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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74 'gene_name': gene['gene_name'],
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75 'detected': False,
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76 'alleles': None,
0
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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77 }
b2d56a44a872 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/screen_abricate_report commit 1d569fc27b052d1982d82ca19455caaff6386f46"
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78 for abricate_report_row in abricate_report_reader:
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79 if detect_gene(abricate_report_row, gene['regex'], args.min_coverage, args.min_identity):
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80 gene_detection_status['detected'] = True
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81 if not gene_detection_status['alleles']:
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82 gene_detection_status['alleles'] = abricate_report_row['GENE']
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83 else:
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84 gene_detection_status['alleles'] = ",".join([
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85 gene_detection_status['alleles'],
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86 abricate_report_row['GENE'],
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87 ])
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88 screened_report_writer.writerow(abricate_report_row)
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89 gene_detection_status_writer.writerow(gene_detection_status)
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90 f1.seek(0) # return file pointer to start of abricate report
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91 next(abricate_report_reader)
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92
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93
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94 if __name__ == '__main__':
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95 parser = argparse.ArgumentParser()
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96 parser.add_argument("abricate_report", help="Input: Abricate report to screen (tsv)")
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97 parser.add_argument("--screening_file", help="Input: List of genes to screen for (tsv)")
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98 parser.add_argument("--screened_report",
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99 help=("Output: Screened abricate report, including only genes of interest (tsv)"))
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100 parser.add_argument("--gene_detection_status",
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101 help=("Output: detection status for all genes listed in the screening file (tsv)"))
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102 parser.add_argument("--min_coverage", type=float, default=90.0,
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103 choices=Range(0.0, 100.0),
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104 help=("Minimum percent coverage (default 90.0)"))
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105 parser.add_argument("--min_identity", type=float, default=90.0,
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106 choices=Range(0.0, 100.0),
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107 help=("Minimum percent identity (default 90.0)"))
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108 parser.add_argument("-v", "--version", action='version', version='%(prog)s 0.4.0')
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109 args = parser.parse_args()
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110 main(args)