--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tbprofiler_json_to_tabular.py	Tue Sep 19 18:03:41 2023 +0000
@@ -0,0 +1,137 @@
+#!/usr/bin/env python
+
+import argparse
+import csv
+import json
+        
+
+def main(args):
+
+    with open(args.input, 'r') as f:
+        report = json.load(f)
+
+    qc_fieldnames = [
+        'pct_reads_mapped',
+        'num_reads_mapped',
+        'median_coverage',
+    ]
+
+    with open(args.qc, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=qc_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        output = {k: report['qc'][k] for k in qc_fieldnames}
+        writer.writerow(output)
+
+    gene_coverage_fieldnames = [
+        'locus_tag',
+        'gene',
+        'fraction',
+        'cutoff',
+    ]
+
+    with open(args.gene_coverage, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=gene_coverage_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        for row in report['qc']['gene_coverage']:
+            writer.writerow(row)
+
+    missing_positions_fieldnames = [
+        'locus_tag',
+        'gene',
+        'position',
+        'variants',
+        'drugs'
+    ]
+
+    with open(args.missing_positions, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=missing_positions_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        for row in report['qc']['missing_positions']:
+            writer.writerow(row)
+
+    resistance_variants_fieldnames = [
+        'chrom',
+        'genome_pos',
+        'locus_tag',
+        'feature_id',
+        'gene',
+        'type',
+        'ref',
+        'alt',
+        'freq',
+        'nucleotide_change',
+        'protein_change',
+        'change',
+        'drugs',
+    ]
+
+    with open(args.resistance_variants, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=resistance_variants_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        for row in report['dr_variants']:
+            row['drugs'] = ', '.join([drug['drug'] + ':' + drug['confers'] for drug in row['drugs']])
+            output = {k: row[k] for k in resistance_variants_fieldnames}
+            writer.writerow(output)
+
+    other_variants_fieldnames = [
+        'chrom',
+        'genome_pos',
+        'locus_tag',
+        'feature_id',
+        'gene',
+        'type',
+        'ref',
+        'alt',
+        'freq',
+        'nucleotide_change',
+        'protein_change',
+        'change',
+        'gene_associated_drugs',
+    ]
+
+    with open(args.other_variants, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=other_variants_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        for row in report['other_variants']:
+            row['gene_associated_drugs'] = ', '.join(row['gene_associated_drugs'])
+            output = {k: row[k] for k in other_variants_fieldnames}
+            writer.writerow(output)
+
+    analysis_metadata_fieldnames = [
+        'timestamp',
+        'tbprofiler_version',
+        'mapping_program',
+        'variant_calling_program',
+        'db_name',
+        'db_commit',
+        'db_date',
+    ]
+
+    with open(args.analysis_metadata, 'w') as f:
+        writer = csv.DictWriter(f, fieldnames=analysis_metadata_fieldnames, dialect='excel-tab', quoting=csv.QUOTE_MINIMAL)
+        writer.writeheader()
+        output = {}
+        output['timestamp'] = report['timestamp']
+        output['tbprofiler_version'] = report['tbprofiler_version']
+        output['db_name'] = report['db_version']['name']
+        output['db_commit'] = report['db_version']['commit']
+        output['db_date'] = report['db_version']['Date']
+        for pipeline_entry in report['pipeline']:
+            if pipeline_entry['Analysis'] == "Mapping":
+                output['mapping_program'] = pipeline_entry['Program']
+            elif pipeline_entry['Analysis'] == "Variant calling":
+                output['variant_calling_program'] = pipeline_entry['Program']
+        
+        writer.writerow(output)
+            
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser()
+    parser.add_argument('input')
+    parser.add_argument('--qc')
+    parser.add_argument('--gene-coverage')
+    parser.add_argument('--missing-positions')
+    parser.add_argument('--resistance-variants')
+    parser.add_argument('--other-variants')
+    parser.add_argument('--analysis-metadata')
+    args = parser.parse_args()
+    main(args)