Mercurial > repos > cstrittmatter > test_eurl_vtec_wgs_pt

annotate scripts/modules/typing.py @ 0:965517909457 draft

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planemo upload commit 15239f1674081ab51ab8dd75a9a40cf1bfaa93e8
author cstrittmatter
date Wed, 22 Jan 2020 08:41:44 -0500
parents
children 0cbed1c0a762
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 import os.path
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2 import functools
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3
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4 import utils
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5
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6 def simplify_data_by_gene(data_by_gene):
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7 cleaned_data_by_gene = {}
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8 for counter, data in data_by_gene.items():
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9 cleaned_data_by_gene[data['header']] = {'gene_identity': data['gene_identity'], 'gene_coverage': data['gene_coverage'], 'gene_depth': data['gene_mean_read_coverage']}
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10 return cleaned_data_by_gene
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13 def possible_types(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth):
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14 data_by_gene = simplify_data_by_gene(data_by_gene)
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15
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16 possible_pathotypes = []
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17 with open(typing_rules_file, 'rtU') as reader:
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18 genes = []
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19 for line in reader:
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20 line = line.splitlines()[0]
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21 if len(line) > 0:
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22 line = line.split('\t')
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23 if line[0].startswith('#'):
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24 genes = map(str.lower, line[1:])
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25 else:
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26 profile = line[1:]
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27 congruence = []
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28 for x, gene_requirement in enumerate(profile):
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29 gene_requirement = True if gene_requirement == '1' else False if gene_requirement == '0' else None
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30 if gene_requirement is None:
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31 congruence.append(True)
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32 else:
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33 if data_by_gene[genes[x]]['gene_coverage'] >= min_gene_coverage and data_by_gene[genes[x]]['gene_identity'] >= min_gene_identity and data_by_gene[genes[x]]['gene_depth'] >= min_gene_depth:
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34 gene_present = True
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35 else:
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36 gene_present = False
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37
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38 if gene_present == gene_requirement:
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39 congruence.append(True)
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40 else:
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41 congruence.append(False)
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42 if all(congruence):
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43 possible_pathotypes.append(line[0])
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44 return possible_pathotypes
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45
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46
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47 module_timer = functools.partial(utils.timer, name='Module Typing')
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48
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49
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50 @module_timer
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51 def typing(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth, outdir):
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52 possible_pathotypes = possible_types(data_by_gene, typing_rules_file, min_gene_coverage, min_gene_identity, min_gene_depth)
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53 with open(os.path.join(outdir, 'patho_typing.report.txt'), 'wt') as writer:
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54 if len(possible_pathotypes) > 0:
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55 writer.write('\n'.join(possible_pathotypes) + '\n')
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56 print '\n' + 'Pathotypes found:' + '\n'
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57 print '\n'.join(possible_pathotypes) + '\n'
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58 else:
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59 writer.write('NA' + '\n')
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60 print '\n' + 'It was not possible to identify any possible pathotype match' + '\n'
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61
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62 return None, None