Mercurial > repos > public-health-bioinformatics > amino2consensus

annotate resistance.py @ 1:88a2b4d2c066 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 66a9f18802686a105b392e73e82c0078d0cdf2a4"
author public-health-bioinformatics
date Wed, 08 Jan 2020 19:36:19 -0500
parents 1e0389317446
children
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
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1 #!/usr/bin/env python
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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3 from __future__ import print_function
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
public-health-bioinformatics
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6 import argparse
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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7 from pprint import pprint
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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8
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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9
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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10 import yaml
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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13 HCV_RULES_VERSION = "1.8"
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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16 def load_rules_config(rules_config, genotype, backup_genotype=None):
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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17 rules = {
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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18 'drug_class': {},
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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19 'drugs': {}
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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20 }
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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21 rules['alg_name'] = 'HCV_RULES'
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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22 rules['alg_version'] = HCV_RULES_VERSION
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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23 rules['level_def'] = {
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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24 '-1': 'Resistance Interpretation Not Available',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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25 '0': 'Sequence does not meet quality-control standards',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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26 '1': 'Likely Susceptible',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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27 '2': 'Not Indicated',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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28 '3': 'Mutations Detected; Effect Unknown',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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29 '4': 'Resistance Possible',
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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30 '5': 'Resistance Likely'
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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31 }
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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32 rules['global_range'] = [('-INF', '3', '1'), ('4', '7', '4'), ('8', 'INF', '5')]
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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33 for drug in rules_config:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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34 drug_code = drug['code']
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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35 drug_rules = []
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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36 region = None
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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37 for genotype_config in drug['genotypes']:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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38 region = genotype_config['region']
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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39 rule_text = genotype_config['rules']
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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40 if genotype_config['genotype'] == genotype:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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41 rules['gene_def'][genotype_config['reference']] = [region]
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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42 break
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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43 elif genotype_config['genotype'] == backup_genotype:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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44 rules['gene_def'].setdefault(genotype_config['reference'], [region])
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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45 break
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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46 else:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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47 rule_text = 'SCORE FROM ( TRUE => "Not available" )'
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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48 drug_rules.append((rule_text, [('scorerange', 'useglobalrange')]))
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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49 try:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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50 rules['drug_class'][region].append(drug_code)
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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51 except KeyError:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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52 rules['drug_class'][region] = [drug_code]
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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53 rules['drugs'][drug_code] = (drug['name'], drug_rules)
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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54 return rules
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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55
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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56
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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57 def main(args):
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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58 with open(args.rules) as f:
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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59 rules = load_rules_config(yaml.safe_load(f), None)
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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60 pprint(rules)
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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61
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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62
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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63 if __name__ == '__main__':
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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64 parser = argparse.ArgumentParser()
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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65 parser.add_argument("consensus", help="Consensus fasta")
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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66 parser.add_argument("--rules", help="Rules file (yaml)")
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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67 args = parser.parse_args()
1e0389317446 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/micall-lite commit 9c3ab5825c19a7c400a46f727975edb480a91c09"
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68 main(args)