Mercurial > repos > public-health-bioinformatics > tbprofiler_json_to_tabular

annotate tbprofiler_json_to_tabular.py @ 0:3e0d5ceeeb0f draft default tip

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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
author public-health-bioinformatics
date Tue, 19 Sep 2023 18:03:41 +0000
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3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
public-health-bioinformatics
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1 #!/usr/bin/env python
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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3 import argparse
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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4 import csv
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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5 import json
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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8 def main(args):
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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10 with open(args.input, 'r') as f:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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11 report = json.load(f)
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3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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13 qc_fieldnames = [
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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14 'pct_reads_mapped',
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15 'num_reads_mapped',
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16 'median_coverage',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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17 ]
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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19 with open(args.qc, 'w') as f:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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20 writer = csv.DictWriter(f, fieldnames=qc_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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21 writer.writeheader()
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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22 output = {k: report['qc'][k] for k in qc_fieldnames}
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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23 writer.writerow(output)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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24
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25 gene_coverage_fieldnames = [
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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26 'locus_tag',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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27 'gene',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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28 'fraction',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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29 'cutoff',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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30 ]
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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31
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32 with open(args.gene_coverage, 'w') as f:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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33 writer = csv.DictWriter(f, fieldnames=gene_coverage_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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34 writer.writeheader()
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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35 for row in report['qc']['gene_coverage']:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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36 writer.writerow(row)
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37
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38 missing_positions_fieldnames = [
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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39 'locus_tag',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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40 'gene',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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41 'position',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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42 'variants',
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43 'drugs'
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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44 ]
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45
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46 with open(args.missing_positions, 'w') as f:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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47 writer = csv.DictWriter(f, fieldnames=missing_positions_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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48 writer.writeheader()
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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49 for row in report['qc']['missing_positions']:
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50 writer.writerow(row)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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51
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52 resistance_variants_fieldnames = [
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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53 'chrom',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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54 'genome_pos',
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55 'locus_tag',
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56 'feature_id',
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57 'gene',
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58 'type',
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59 'ref',
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60 'alt',
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61 'freq',
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62 'nucleotide_change',
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63 'protein_change',
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64 'change',
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65 'drugs',
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66 ]
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67
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68 with open(args.resistance_variants, 'w') as f:
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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69 writer = csv.DictWriter(f, fieldnames=resistance_variants_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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70 writer.writeheader()
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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71 for row in report['dr_variants']:
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72 row['drugs'] = ', '.join([drug['drug'] + ':' + drug['confers'] for drug in row['drugs']])
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73 output = {k: row[k] for k in resistance_variants_fieldnames}
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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74 writer.writerow(output)
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75
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76 other_variants_fieldnames = [
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77 'chrom',
3e0d5ceeeb0f planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
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78 'genome_pos',
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79 'locus_tag',
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80 'feature_id',
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81 'gene',
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82 'type',
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83 'ref',
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84 'alt',
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85 'freq',
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86 'nucleotide_change',
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87 'protein_change',
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88 'change',
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89 'gene_associated_drugs',
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90 ]
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91
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92 with open(args.other_variants, 'w') as f:
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93 writer = csv.DictWriter(f, fieldnames=other_variants_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
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94 writer.writeheader()
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95 for row in report['other_variants']:
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96 row['gene_associated_drugs'] = ', '.join(row['gene_associated_drugs'])
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97 output = {k: row[k] for k in other_variants_fieldnames}
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98 writer.writerow(output)
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99
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100 analysis_metadata_fieldnames = [
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101 'timestamp',
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102 'tbprofiler_version',
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103 'mapping_program',
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104 'variant_calling_program',
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105 'db_name',
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106 'db_commit',
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107 'db_date',
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108 ]
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109
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110 with open(args.analysis_metadata, 'w') as f:
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111 writer = csv.DictWriter(f, fieldnames=analysis_metadata_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
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112 writer.writeheader()
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113 output = {}
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114 output['timestamp'] = report['timestamp']
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115 output['tbprofiler_version'] = report['tbprofiler_version']
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116 output['db_name'] = report['db_version']['name']
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117 output['db_commit'] = report['db_version']['commit']
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118 output['db_date'] = report['db_version']['Date']
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119 for pipeline_entry in report['pipeline']:
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120 if pipeline_entry['Analysis'] == "Mapping":
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121 output['mapping_program'] = pipeline_entry['Program']
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122 elif pipeline_entry['Analysis'] == "Variant calling":
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123 output['variant_calling_program'] = pipeline_entry['Program']
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124
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125 writer.writerow(output)
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126
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127 if __name__ == '__main__':
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128 parser = argparse.ArgumentParser()
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129 parser.add_argument('input')
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130 parser.add_argument('--qc')
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131 parser.add_argument('--gene-coverage')
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132 parser.add_argument('--missing-positions')
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133 parser.add_argument('--resistance-variants')
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134 parser.add_argument('--other-variants')
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135 parser.add_argument('--analysis-metadata')
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136 args = parser.parse_args()
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137 main(args)