From e7cf4068fc6b0aa2aaffce41bc719b3cf9066c97 Mon Sep 17 00:00:00 2001 From: Peter van Heusden Date: Fri, 31 May 2024 15:50:28 +0200 Subject: [PATCH] Update to support TB-Profiler 6 --- galaxy/test-data/rif_resistant.results.json | 294051 ++++++++++++++- setup.py | 4 +- tbvcfreport/dbconn.py | 2 +- tbvcfreport/report.py | 30 +- tbvcfreport/tbprofiler.py | 77 +- tbvcfreport/tbvcfreport.py | 14 +- tbvcfreport/templates/base.html | 28 +- .../templates/drug_resistance_report.html | 57 +- tbvcfreport/vcfproc.py | 5 + test/test_cli.py | 1 + 10 files changed, 294192 insertions(+), 77 deletions(-) diff --git a/galaxy/test-data/rif_resistant.results.json b/galaxy/test-data/rif_resistant.results.json index dfafbdc..135cf3c 100644 --- a/galaxy/test-data/rif_resistant.results.json +++ b/galaxy/test-data/rif_resistant.results.json @@ -1 +1,294050 @@ -{"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], 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Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Leu43fs" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 779117, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Leu43fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Leu43fs" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 779118, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Leu43fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Leu43fs" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 779119, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Leu44fs", + "confidence": "Assoc w R - 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Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46Arg" + }, + { + "type": "drug_resistance", + "drug": "clofazimine", + "original_mutation": "p.Cys46Arg", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46Arg" + }, + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Cys46fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Includes data from one site that only submitted resistant strains, which may have inflated the PPV. Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46fs" + }, + { + "type": "drug_resistance", + "drug": "clofazimine", + "original_mutation": "p.Cys46fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46fs" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 779126, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Cys46Arg", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Includes data from one site that only submitted resistant strains, which may have inflated the PPV. 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Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46fs" + }, + { + "type": "drug_resistance", + "drug": "clofazimine", + "original_mutation": "p.Cys46fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Can only confer resistance if genetically linked to a functional MmpL5", + "gene": "Rv0678", + "variant": "p.Cys46fs" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 779127, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "bedaquiline", + "original_mutation": "p.Cys46Arg", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "Includes data from one site that only submitted resistant strains, which may have inflated the PPV. 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"confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407776, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407777, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": 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"type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Ala134Glu", + "confidence": "Assoc w R", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Ala134Glu" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407804, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Ala133fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Ala133fs" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407805, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Ala133fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Ala133fs" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from 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"pos": 4407811, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407812, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407813, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407814, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": 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"drug": "streptomycin", + "original_mutation": "p.Gly129fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Gly129fs" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.386_388delGCGinsCC", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.386_388delGCGinsCC" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407817, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + 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"drug": "streptomycin", + "original_mutation": "p.Trp123*", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Trp123*" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407836, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Trp123*", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Trp123*" + }, + { + "type": "drug_resistance", + "drug": 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"c.351_446delGCGCGCCGAGGAGTCCTGGGTGCAGGACCAATTGGGCGGCAGCGACGCTGCGGTGTCACGGGCGGTGGCCGCGTTGGACAAGTTGACGAAATGGAG" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.330_356delGGCCGTTGAGATCGTGCGGGGGCGCGCinsTGCCGTTGAGATCGTGCGGGGGCGCG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.330_356delGGCCGTTGAGATCGTGCGGGGGCGCGCinsTGCCGTTGAGATCGTGCGGGGGCGCG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407850, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Arg118fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + 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"Chromosome", + "pos": 4407853, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "p.Gly117fs", + "confidence": "Assoc w R - Interim", + "source": "WHO catalogue v2", + "comment": "", + "gene": "Rv3919c", + "variant": "p.Gly117fs" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.336_359dupTGAGATCGTGCGGGGGCGCGCCGA" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.330_356delGGCCGTTGAGATCGTGCGGGGGCGCGCinsTGCCGTTGAGATCGTGCGGGGGCGCG", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.330_356delGGCCGTTGAGATCGTGCGGGGGCGCGCinsTGCCGTTGAGATCGTGCGGGGGCGCG" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4407854, + "depth": 0, + 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"c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408256, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408257, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408258, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408259, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408260, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408261, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408262, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408263, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408264, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408265, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408266, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408267, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408268, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408269, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408270, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408271, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408272, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-70_140del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-70_140del" + }, + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408273, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408274, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408275, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + }, + { + "chrom": "Chromosome", + "pos": 4408276, + "depth": 0, + "annotation": [ + { + "type": "drug_resistance", + "drug": "streptomycin", + "original_mutation": "c.-74_319del", + "confidence": "", + "source": "tbdb", + "comment": "Mutation from literature", + "gene": "Rv3919c", + "variant": "c.-74_319del" + } + ] + } + ] + }, + "linked_samples": [] +} \ No newline at end of file diff --git a/setup.py b/setup.py index ab5a90d..0921d3b 100644 --- a/setup.py +++ b/setup.py @@ -5,7 +5,7 @@ setup( name="tbvcfreport", - version="0.1.8", + version="0.2.0", url="https://github.com/COMBAT-TB/tbvcfreport", author="SANBI", author_email="help@sanbi.ac.za", @@ -19,7 +19,7 @@ package_data={ "tbvcfreport": ["templates/*.html"], }, - python_requires=">=3.6", + python_requires=">=3.10", install_requires=[ "click", "neo4j", diff --git a/tbvcfreport/dbconn.py b/tbvcfreport/dbconn.py index 6d11090..33e9141 100644 --- a/tbvcfreport/dbconn.py +++ b/tbvcfreport/dbconn.py @@ -37,5 +37,5 @@ def _get_gene_table_tx(tx, genes=None): def query_by_gene_list(self, gene_list): with self.driver.session() as session: - values = session.read_transaction(self._get_gene_table_tx, gene_list) + values = session.execute_read(self._get_gene_table_tx, gene_list) return values diff --git a/tbvcfreport/report.py b/tbvcfreport/report.py index 720be1f..12d719b 100644 --- a/tbvcfreport/report.py +++ b/tbvcfreport/report.py @@ -62,18 +62,17 @@ def generate_txt_report(file_name, data): """ v_txt_output = "{file_name}_variants_report.txt".format(file_name=file_name) - lineage_header = ["Lineage", "Family", "Spoligotype", "RD", "Agreement"] - lineage_data = [] - for lineage in data["lineage"]: + lineage_header = [] + if "lineage" in data and "lineage" in data["lineage"]: + lineage_header = ["Lineage", "Support", "Family", "RD"] + lineage_data = [] lineage_data.append( - [ - lineage["lin"], - lineage["family"], - lineage["spoligotype"], - lineage["rd"], - str(lineage["frac"]), - ] + [ str(el) for el in data["lineage"]["lineage"] ] ) + if "sub_lineage" in data["lineage"]: + lineage_data.append( + [ str(el) for el in data["lineage"]["sub_lineage"] ] + ) variants_header = [ "CHR", @@ -112,9 +111,10 @@ def generate_txt_report(file_name, data): with open(v_txt_output, "w") as _variants_report: _variants_report.write("#{} Report\n".format(file_name.capitalize())) - _variants_report.write("#{}\n".format("\t".join(lineage_header))) - for l_data in lineage_data: - _variants_report.write("{}\n".format("\t".join(l_data))) + if lineage_header: + _variants_report.write("#{}\n".format("\t".join(lineage_header))) + for l_data in lineage_data: + _variants_report.write("{}\n".format("\t".join(l_data))) _variants_report.write("\n#{}\n".format("\t".join(variants_header))) for variant in variants: @@ -131,7 +131,7 @@ def generate_txt_report(file_name, data): for l_data in lineage_data: dr_report.write("{}\n".format("\t".join(l_data))) - dr_report.write("\n#TBProfiler Drug Resistance Report\n") + dr_report.write("\n#TB-Profiler Drug Resistance Report\n") dr_report.write( "\n#{}\n".format( "\t".join(["Drug", "Resistance", "Supporting Mutations"]) @@ -152,5 +152,5 @@ def generate_txt_report(file_name, data): "{}\n".format("\t".join([drug, resistant, ",".join(mutations)])) ) dr_report.write( - "\n#Drug resistance predictions are for research purposes only and are produced by the TBProfiler software.\n" + "\n#Drug resistance predictions are for research purposes only and are produced by the TB-Profiler software.\n" ) diff --git a/tbvcfreport/tbprofiler.py b/tbvcfreport/tbprofiler.py index 60547c9..a1bd0bd 100644 --- a/tbvcfreport/tbprofiler.py +++ b/tbvcfreport/tbprofiler.py @@ -1,4 +1,5 @@ """Interface to TBProfiler report.""" +from typing import TextIO import json @@ -11,17 +12,20 @@ "pyrazinamide", "streptomycin", "ethionamide", - "fluoroquinolones", + "fluoroquinolones", # this is present in older versions of tbdb "amikacin", "capreomycin", "kanamycin", "para-aminosalicylic_acid", "cycloserine", - "delaminid", + "delamanid", "linezolid", "clofazimine", "bedaquiline", - "aminoglycosides" + "aminoglycosides" # this is present in newer versions of tbdb + "levofloxacin", + "moxifloxacin", + "pretomanid" ] drug_names = { @@ -31,29 +35,32 @@ "pyrazinamide": "Pyrazinamide", "streptomycin": "Streptomycin", "ethionamide": "Ethionamide", - "fluoroquinolones": "Fluoroquinolones", + "fluoroquinolones": "Fluoroquinolones", # this is present in older versions of tbdb "amikacin": "Amikacin", "capreomycin": "Capreomycin", "kanamycin": "Kanamycin", "para-aminosalicylic_acid": "Para-aminosalicylic acid", "linezolid": "Linezolid", "cycloserine": "Cycloserine", - "delaminid": "Delaminid", + "delamanid": "Delamanid", "clofazimine": "Clofazimine", "bedaquiline": "Bedaquiline", - "aminoglycosides": "Aminoglycosides" + "aminoglycosides": "Aminoglycosides", # this is present in newer versions of tbdb + "levofloxacin": "Levofloxacin", + "moxifloxacin": "Moxifloxacin", + "pretomanid": "Pretomanid" } class TBProfilerReport: """Process tbprofiler_report.""" - def __init__(self, json_file, _variants): + def __init__(self, json_file: TextIO, _variants: list[list]): """initializer.""" self.json_file = json_file self._variants = _variants - def get_data(self): + def get_data(self) -> tuple[list[str], dict, int, str, dict[str, str]]: """Get TBProfiler data.""" drug_resistance_list, call_positions = [], set() rrs_start, rrs_end = 1471846, 1473382 @@ -64,10 +71,44 @@ def get_data(self): rrs_variant_count += 1 call_positions.add(POS) tbprofiler_data = json.load(self.json_file) - tbprofiler_version = tbprofiler_data["tbprofiler_version"] - tbprofiler_major_version = int(tbprofiler_version.split(".")[0]) + if "tbprofiler_version" in tbprofiler_data: + tbprofiler_version = tbprofiler_data["tbprofiler_version"] + else: + tbprofiler_version = tbprofiler_data["pipeline"]["software_version"] + tbprofiler_major_version= int(tbprofiler_version.split(".")[0]) + + if tbprofiler_major_version < 3: + tbdb_version = {} + for key in ("name", "commit", "author", "date"): + tbdb_version[key] = "Unknown" + elif tbprofiler_major_version < 4: + tbdb_version = tbprofiler_data["db_version"] + else: + tbdb_version = tbprofiler_data["pipeline"]["db_version"] # dict with keys: name, commit, author, date dr_data = tbprofiler_data["dr_variants"] - lineage = tbprofiler_data["lineage"] + + if tbprofiler_major_version < 4: + main_lineage_key = "main_lin" + sublineage_key = "sublin" + lineage_key = "lin" + fraction_key = "frac" + else: + main_lineage_key = "main_lineage" + sublineage_key = "sub_lineage" + lineage_key = "lineage" + fraction_key = "fraction" + lineage_details = {} + for lineage in tbprofiler_data["lineage"]: + lineage_details[lineage[lineage_key]] = (lineage[lineage_key], + lineage[fraction_key], + lineage["family"], + "" if lineage["rd"] is None else lineage["rd"]) + lineage_info = { + "lineage": lineage_details[tbprofiler_data[main_lineage_key]] + } + if sublineage_key in tbprofiler_data: + lineage_info["sub_lineage"] = lineage_details[tbprofiler_data[sublineage_key]] + _drug_resistance = self._drug_resistance( dr_data, call_positions, tbprofiler_major_version ) @@ -82,15 +123,17 @@ def get_data(self): "resistant": False, } ) - return (drug_resistance_list, lineage, rrs_variant_count) + return (drug_resistance_list, lineage_info, rrs_variant_count, tbprofiler_version, tbdb_version) @staticmethod - def _drug_resistance(_dr_data, call_positions, tbprofiler_version): + def _drug_resistance(_dr_data: dict, call_positions: list[int], tbprofiler_version: int) -> dict: dr_calls_seen, drug_resistance = set(), {} + position_key = "genome_pos" if tbprofiler_version < 4 else "pos" + gene_name_key = "gene" if tbprofiler_version < 4 else "gene_name" for record in _dr_data: - if record["genome_pos"] in dr_calls_seen: + if record[position_key] in dr_calls_seen: continue - dr_calls_seen.add(record["genome_pos"]) + dr_calls_seen.add(record[position_key]) if tbprofiler_version < 3: variant_drug_names = [record["drug"]] else: @@ -109,10 +152,10 @@ def _drug_resistance(_dr_data, call_positions, tbprofiler_version): "variants": [], }, ) - if record["genome_pos"] not in call_positions: + if record[position_key] not in call_positions: dr_record["snippy_agreement"] = False dr_record["variants"].append( - (record["gene"], record["change"], round(record["freq"], 2)) + (record[gene_name_key], record["change"], round(record["freq"], 2)) # round to 2 digits ) drug_resistance[drug_name] = dr_record return drug_resistance diff --git a/tbvcfreport/tbvcfreport.py b/tbvcfreport/tbvcfreport.py index 8f9862f..8e16e88 100644 --- a/tbvcfreport/tbvcfreport.py +++ b/tbvcfreport/tbvcfreport.py @@ -33,7 +33,12 @@ def parse_and_generate_report(vcf_file, filter_udi, db_url, json_report=None): lineage = {} vcf_base_name = os.path.basename(vcf_file) (vcf_file_name, ext) = os.path.splitext(vcf_base_name) - click.secho(f"Processing {vcf_base_name}...\n", fg="green") + if json_report is not None: + dr_reporting = "with DR reporting" + else: + dr_reporting = "" + + click.secho(f"Processing {vcf_base_name} {dr_reporting}... \n", fg="green") vcf_proc = VCFProc(vcf_file=vcf_file, db_url=db_url, filter_udi=filter_udi) variants = vcf_proc.parse() @@ -45,12 +50,17 @@ def parse_and_generate_report(vcf_file, filter_udi, db_url, json_report=None): raise TypeError(f"Expected a json file. Found {json_base_name}!") tbprofiler = TBProfilerReport(json_report, variants) - (drug_resistance_list, lineage, rrs_variant_count) = tbprofiler.get_data() + (drug_resistance_list, lineage, rrs_variant_count, tbprofiler_version, tbdb_version) = tbprofiler.get_data() + else: + tbprofiler_version = "N/A" + tbdb_version = "N/A" data = { "variants": variants, "lineage": lineage, "dr_data": drug_resistance_list, "mixed_infection": rrs_variant_count > 1, + "tbprofiler_version": tbprofiler_version, + "tbdb_version": tbdb_version, } generate_report(file_name=vcf_file_name, data=data) diff --git a/tbvcfreport/templates/base.html b/tbvcfreport/templates/base.html index 6fe1852..9e31b08 100644 --- a/tbvcfreport/templates/base.html +++ b/tbvcfreport/templates/base.html @@ -25,29 +25,29 @@

{% if 'lineage' in data and data['lineage']['lineage'] %}
- +
- - - + + + - - - - + {% for element in data['lineage']['lineage'] %} + + {% endfor %} + {% if 'sub_lineage' in data['lineage'] and data['lineage']['sub_lineage'] %} + + {% for element in data['lineage']['sub_lineage'] %} + + {% endfor %} + + {% endif %}
Lineage Info
Species LineageSub-lineageAgreement with SNPs from this lineageLineage support fractionFamilyRD
{{ data['lineage']['species'] }}{{ data['lineage']['lineage'] }} - {% if data['lineage']['sublineage'] %} - {{ data['lineage']['sublineage'] }} - {% else %} - Not Available - {% endif %} - {{ data['lineage']['percent_agreement'] }}%{{ element }}
{{ element }}
diff --git a/tbvcfreport/templates/drug_resistance_report.html b/tbvcfreport/templates/drug_resistance_report.html index 3103c50..71fcbc9 100644 --- a/tbvcfreport/templates/drug_resistance_report.html +++ b/tbvcfreport/templates/drug_resistance_report.html @@ -3,37 +3,44 @@

TBProfiler + rel="noreferrer noopener">TB-Profiler Drug Resistance Report

- - - +
+

TB-Profiler version {{ data["tbprofiler_version"] }} with + database {{ data["tbdb_version"]["name"] + ':' + data["tbdb_version"]["commit"]}} ({{ data["tbdb_version"]["Date"] }})

+
+
+
+
- Disclaimer: - Drug resistance predictions are for Research Purposes Only and are produced by - TBProfiler. -
+ + + + + + + + + {% for entry in data['dr_data'] %} - - - + + + - - {% for entry in data['dr_data'] %} - - - - - - {% endfor %} -
+ Disclaimer: + Drug resistance predictions are for Research Purposes Only and are produced by + TB-Profiler. +
DrugResistanceSupporting Mutations
DrugResistanceSupporting Mutations{{ entry['drug_human_name'] }}{% if entry['resistant'] %}R{% else %}S{% endif %}{% for mutation in entry['variants'] %} + {{ mutation[0] }} + ({{ mutation[2] }} {{ mutation[1] }}) + {% endfor %}
{{ entry['drug_human_name'] }}{% if entry['resistant'] %}R{% else %}S{% endif %}{% for mutation in entry['variants'] %} - {{ mutation[0] }} - ({{ mutation[2] }} {{ mutation[1] }}) - {% endfor %}
+ {% endfor %} + +
{% endif %} {% endblock %} diff --git a/tbvcfreport/vcfproc.py b/tbvcfreport/vcfproc.py index 12b0edf..1a093ac 100644 --- a/tbvcfreport/vcfproc.py +++ b/tbvcfreport/vcfproc.py @@ -13,6 +13,11 @@ def __init__(self, vcf_file, db_url, filter_udi=None): self.db = CombatTbDb(db_url, "", "") self.filter_udi = filter_udi + + def __del__(self): + self.db.close() + + def parse(self): """Parse VCF.""" variants, rv_tags = [], [] diff --git a/test/test_cli.py b/test/test_cli.py index 9a14c7d..52cdd9f 100644 --- a/test/test_cli.py +++ b/test/test_cli.py @@ -11,6 +11,7 @@ TEST_TBP_2 = os.path.join(TEST_DATA_DIR, "tb_profiler_2.json") TEST_TBP_3 = os.path.join(TEST_DATA_DIR, "tb_profiler_3.json") EMPTY_VCF = os.path.join(TEST_DATA_DIR, "empty.vcf") +# GALAXY_TEST_DATA contains a report from TB-Profiler 6 GALAXY_TEST_DATA = os.path.join(os.path.dirname(CURR_DIR), "galaxy/test-data/") OUT_DIR = os.path.dirname(CURR_DIR) OUT_TXT_FILE = os.path.join(OUT_DIR, "test_variants_report.txt")