From 3428202688483df6ccf8efa71de80c9aba2da501 Mon Sep 17 00:00:00 2001 From: Jody Phelan Date: Fri, 21 Jun 2024 16:38:29 +0200 Subject: [PATCH] adding in depth to txt output --- tbprofiler/text.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/tbprofiler/text.py b/tbprofiler/text.py index 9dbad98..8de812c 100644 --- a/tbprofiler/text.py +++ b/tbprofiler/text.py @@ -127,9 +127,9 @@ def write_text( summary_table = pp.get_dr_summary(result.dr_variants,conf) text_strings["notes"] = "\n".join(result.notes) text_strings["dr_report"] = pp.dict_list2text(summary_table,sep=sep) - text_strings["dr_var_report"] = pp.object_list2text(result.dr_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","freq":"Estimated fraction","drugs.drug":"Drug","drugs.confidence":"Confidence","drugs.comment":"Comment"},sep=sep) - text_strings["other_var_report"] = pp.object_list2text(result.other_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","freq":"Estimated fraction","annotation.drug":"Gene associated drug","annotation.confidence":"Confidence","annotation.comment":"Comment"},sep=sep) - text_strings["qc_fail_var_report"] = pp.object_list2text(result.qc_fail_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","freq":"Estimated fraction","annotation.drug":"Gene associated drug","annotation.confidence":"Confidence","annotation.comment":"Comment"},sep=sep) + text_strings["dr_var_report"] = pp.object_list2text(result.dr_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","depth": "Depth","freq":"Estimated fraction","drugs.drug":"Drug","drugs.confidence":"Confidence","drugs.comment":"Comment"},sep=sep) + text_strings["other_var_report"] = pp.object_list2text(result.other_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","depth": "Depth","freq":"Estimated fraction","annotation.drug":"Gene associated drug","annotation.confidence":"Confidence","annotation.comment":"Comment"},sep=sep) + text_strings["qc_fail_var_report"] = pp.object_list2text(result.qc_fail_variants,mappings={"pos":"Genome Position","gene_id":"Locus Tag",'gene_name':'Gene name',"type":"Variant type","change":"Change","depth": "Depth","freq":"Estimated fraction","annotation.drug":"Gene associated drug","annotation.confidence":"Confidence","annotation.comment":"Comment"},sep=sep) text_strings["coverage_report"] = result.get_qc() text_strings['lineage_report'] = pp.object_list2text(result.lineage,mappings={"lineage":"Lineage","fraction":"Fraction","family":"Family","rd":"rd"},sep=sep)#result.lineage) text_strings['strain'] = result.sub_lineage