diff --git a/db/tbdb.bed b/db/tbdb.bed index 65b8112..5ff20c7 100644 --- a/db/tbdb.bed +++ b/db/tbdb.bed @@ -2,9 +2,9 @@ Chromosome 1 1524 Rv0001 dnaA isoniazid Chromosome 4933 7267 Rv0005 gyrB levofloxacin,moxifloxacin Chromosome 7068 9818 Rv0006 gyrA levofloxacin,moxifloxacin Chromosome 13133 13911 Rv0010c Rv0010c isoniazid -Chromosome 490545 491793 Rv0407 fgd1 pretomanid,delamanid,clofazimine -Chromosome 574479 576790 Rv0486 mshA isoniazid,ethionamide -Chromosome 619500 620865 Rv0529 ccsA kanamycin,capreomycin,amikacin +Chromosome 490545 491793 Rv0407 fgd1 clofazimine,delamanid,pretomanid +Chromosome 574479 576790 Rv0486 mshA ethionamide,isoniazid +Chromosome 619500 620865 Rv0529 ccsA amikacin,capreomycin,kanamycin Chromosome 656010 657739 Rv0565c Rv0565c ethionamide Chromosome 731680 732406 Rv0635 hadA isoniazid Chromosome 733853 734970 Rv0639 nusG rifampicin @@ -16,52 +16,52 @@ Chromosome 778477 779624 Rv0677c mmpS5 bedaquiline,clofazimine Chromosome 778790 779487 Rv0678 mmpR5 bedaquiline,clofazimine Chromosome 781126 781934 Rv0682 rpsL streptomycin Chromosome 800106 801462 Rv0701 rplC linezolid -Chromosome 1253074 1254783 Rv1129c Rv1129c levofloxacin,moxifloxacin,isoniazid,rifampicin -Chromosome 1302606 1305501 Rv1173 fbiC pretomanid,delamanid,clofazimine +Chromosome 1253074 1254783 Rv1129c Rv1129c isoniazid,levofloxacin,moxifloxacin,rifampicin +Chromosome 1302606 1305501 Rv1173 fbiC clofazimine,delamanid,pretomanid Chromosome 1364162 1365186 Rv1221 sigE pyrazinamide -Chromosome 1406081 1407604 Rv1258c Rv1258c streptomycin,pyrazinamide,isoniazid +Chromosome 1406081 1407604 Rv1258c Rv1258c isoniazid,pyrazinamide,streptomycin Chromosome 1416181 1418048 Rv1267c embR ethambutol Chromosome 1460802 1461290 Rv1305 atpE bedaquiline -Chromosome 1471498 1473382 EBG00000313325 rrs kanamycin,capreomycin,streptomycin,amikacin +Chromosome 1471498 1473382 EBG00000313325 rrs amikacin,capreomycin,kanamycin,streptomycin Chromosome 1473408 1476795 EBG00000313339 rrl capreomycin,linezolid -Chromosome 1673148 1675011 Rv1484 inhA isoniazid,ethionamide +Chromosome 1673148 1675011 Rv1484 inhA ethionamide,isoniazid Chromosome 1833247 1834987 Rv1630 rpsA pyrazinamide Chromosome 1853358 1854388 Rv1644 tsnR linezolid Chromosome 1917506 1918746 Rv1694 tlyA capreomycin -Chromosome 2062809 2065010 Rv1819c bacA kanamycin,capreomycin,streptomycin,amikacin -Chromosome 2101651 2103337 Rv1854c ndh isoniazid,delamanid,ethionamide +Chromosome 2062809 2065010 Rv1819c bacA amikacin,capreomycin,kanamycin,streptomycin +Chromosome 2101651 2103337 Rv1854c ndh delamanid,ethionamide,isoniazid Chromosome 2153889 2156842 Rv1908c katG isoniazid Chromosome 2167649 2170934 Rv1918c PPE35 pyrazinamide Chromosome 2221719 2223825 Rv1979c Rv1979c bedaquiline,clofazimine Chromosome 2288681 2290323 Rv2043c pncA pyrazinamide Chromosome 2517915 2519365 Rv2245 kasA isoniazid -Chromosome 2714124 2715832 Rv2416c eis kanamycin,amikacin +Chromosome 2714124 2715832 Rv2416c eis amikacin,kanamycin Chromosome 2725899 2726780 Rv2428 ahpC isoniazid Chromosome 2746135 2747798 Rv2447c folC para-aminosalicylic_acid -Chromosome 2782366 2786169 Rv2477c Rv2477c kanamycin,levofloxacin,moxifloxacin,streptomycin,rifampicin,ethambutol,amikacin +Chromosome 2782366 2786169 Rv2477c Rv2477c amikacin,ethambutol,kanamycin,levofloxacin,moxifloxacin,rifampicin,streptomycin Chromosome 2859300 2860640 Rv2535c pepQ bedaquiline,clofazimine Chromosome 2986639 2987615 Rv2671 ribD para-aminosalicylic_acid Chromosome 2995772 2996737 Rv2680 Rv2680 capreomycin Chromosome 2996539 2998055 Rv2681 Rv2681 capreomycin -Chromosome 3064515 3067372 Rv2752c Rv2752c levofloxacin,moxifloxacin,isoniazid,rifampicin,ethambutol +Chromosome 3064515 3067372 Rv2752c Rv2752c ethambutol,isoniazid,levofloxacin,moxifloxacin,rifampicin Chromosome 3067193 3068161 Rv2754c thyX para-aminosalicylic_acid Chromosome 3073680 3074671 Rv2764c thyA para-aminosalicylic_acid Chromosome 3086620 3087935 Rv2780 ald cycloserine -Chromosome 3338868 3339762 Rv2983 fbiD pretomanid,delamanid,clofazimine +Chromosome 3338868 3339762 Rv2983 fbiD clofazimine,delamanid,pretomanid Chromosome 3448253 3449991 Rv3083 Rv3083 ethionamide -Chromosome 3568401 3569280 Rv3197A whiB7 kanamycin,amikacin,streptomycin +Chromosome 3568401 3569280 Rv3197A whiB7 amikacin,kanamycin,streptomycin Chromosome 3611959 3613847 Rv3236c Rv3236c pyrazinamide -Chromosome 3623159 3625110 Rv3244c lpqB rifampicin,bedaquiline -Chromosome 3624910 3626860 Rv3245c mtrB rifampicin,bedaquiline -Chromosome 3626663 3627924 Rv3246c mtrA rifampicin,bedaquiline -Chromosome 3640207 3641538 Rv3261 fbiA pretomanid,delamanid,clofazimine -Chromosome 3641335 3642881 Rv3262 fbiB pretomanid,delamanid,clofazimine +Chromosome 3623159 3625110 Rv3244c lpqB bedaquiline,rifampicin +Chromosome 3624910 3626860 Rv3245c mtrB bedaquiline,rifampicin +Chromosome 3626663 3627924 Rv3246c mtrA bedaquiline,rifampicin +Chromosome 3640207 3641538 Rv3261 fbiA clofazimine,delamanid,pretomanid +Chromosome 3641335 3642881 Rv3262 fbiB clofazimine,delamanid,pretomanid Chromosome 3840194 3841620 Rv3423c alr cycloserine Chromosome 3877464 3879240 Rv3457c rpoA rifampicin -Chromosome 3986612 3987299 Rv3547 ddn pretomanid,delamanid +Chromosome 3986612 3987299 Rv3547 ddn delamanid,pretomanid Chromosome 4038158 4041013 Rv3596c clpC1 pyrazinamide Chromosome 4043862 4046428 Rv3601c panD pyrazinamide -Chromosome 4138202 4140002 Rv3696c glpK levofloxacin,moxifloxacin,isoniazid,streptomycin,rifampicin,ethambutol +Chromosome 4138202 4140002 Rv3696c glpK ethambutol,isoniazid,levofloxacin,moxifloxacin,rifampicin,streptomycin Chromosome 4237683 4243147 Rv3793 embC ethambutol Chromosome 4242947 4246517 Rv3794 embA ethambutol Chromosome 4246314 4249810 Rv3795 embB ethambutol @@ -69,5 +69,5 @@ Chromosome 4266953 4269124 Rv3805c aftB ethambutol Chromosome 4268925 4270084 Rv3806c ubiA ethambutol Chromosome 4326004 4330174 Rv3854c ethA ethionamide Chromosome 4327328 4328199 Rv3855 ethR ethionamide -Chromosome 4338171 4338961 Rv3862c whiB6 kanamycin,capreomycin,amikacin +Chromosome 4338171 4338961 Rv3862c whiB6 amikacin,capreomycin,kanamycin Chromosome 4407528 4408481 Rv3919c gid streptomycin diff --git a/db/tbdb.dict b/db/tbdb.dict deleted file mode 100644 index 651209f..0000000 --- a/db/tbdb.dict +++ /dev/null @@ -1,2 +0,0 @@ -@HD VN:1.6 -@SQ SN:Chromosome LN:4411532 M5:57b12ff2773c5fd3a0f879972f176e50 UR:file:/Users/jody/github/TBProfiler/db/tbdb.fasta diff --git a/db/tbdb.dr.json b/db/tbdb.dr.json index 0af4a55..09175cc 100644 --- a/db/tbdb.dr.json +++ b/db/tbdb.dr.json @@ -1 +1 @@ -{"Rv1819c": {"c.102G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.102G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.102G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064627], "chromosome": "Chromosome"}, "c.1044G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1044G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063685], "chromosome": "Chromosome"}, "c.105C>G": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.105C>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064624], "chromosome": "Chromosome"}, "c.1065T>G": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1065T>G", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063664], "chromosome": "Chromosome"}, "c.1080G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1080G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063649], "chromosome": "Chromosome"}, "c.1140G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1140G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063589], "chromosome": "Chromosome"}, "c.1170G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1170G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063559], "chromosome": "Chromosome"}, "c.1194C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1194C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063535], "chromosome": "Chromosome"}, "c.1210C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1210C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063519], "chromosome": "Chromosome"}, "c.1212G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1212G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063517], "chromosome": "Chromosome"}, "c.1212G>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1212G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063517], "chromosome": "Chromosome"}, "c.1242G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1242G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063487], "chromosome": "Chromosome"}, "c.129T>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.129T>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064600], "chromosome": "Chromosome"}, "c.1317C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1317C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063412], "chromosome": "Chromosome"}, "c.1323G>C": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1323G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1323G>C", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063406], "chromosome": "Chromosome"}, "c.1348C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1348C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063381], "chromosome": "Chromosome"}, "c.135G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.135G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.135G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2064594], "chromosome": "Chromosome"}, "c.1371G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1371G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": 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assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063324], "chromosome": "Chromosome"}, "c.1426C>T": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1426C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "kanamycin", "original_mutation": "c.1426C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "streptomycin", "original_mutation": "c.1426C>T", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}], "genome_positions": [2063303], "chromosome": "Chromosome"}, "c.1428G>A": {"annotations": [{"type": "who_confidence", "drug": "amikacin", "original_mutation": "c.1428G>A", "confidence": "Not assoc w R - Interim", "source": "WHO catalogue v2", "comment": ""}, {"type": "who_confidence", "drug": "capreomycin", "original_mutation": 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"genome_positions": [3074361], "chromosome": "Chromosome"}, "p.Arg222Gly": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg222Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3073808, 3073807, 3073806], "chromosome": "Chromosome"}, "p.Arg235Pro": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg235Pro", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3073769, 3073768, 3073767], "chromosome": "Chromosome"}, "p.Trp83Cys": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Trp83Cys", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074225, 3074224, 3074223], "chromosome": "Chromosome"}, "p.Gly76*": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Gly76*", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074246, 3074245, 3074244], "chromosome": "Chromosome"}, "c.472delC": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "c.472delC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074000], "chromosome": "Chromosome"}, "p.Val77Phe": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Val77Phe", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074243, 3074242, 3074241], "chromosome": "Chromosome"}, "c.218_219insCACGAGCAC": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "c.218_219insCACGAGCAC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074253, 3074254], "chromosome": "Chromosome"}, "p.Thr22Ala": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Thr22Ala", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074408, 3074407, 3074406], "chromosome": "Chromosome"}, "p.Trp98*": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Trp98*", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074180, 3074179, 3074178], "chromosome": "Chromosome"}, "p.Pro224Leu": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Pro224Leu", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3073802, 3073801, 3073800], "chromosome": "Chromosome"}, "transcript_ablation": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "transcript_ablation", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": null, "chromosome": "Chromosome"}, "p.Cys161Tyr": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Cys161Tyr", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3073991, 3073990, 3073989], "chromosome": "Chromosome"}, "p.Phe152Val": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Phe152Val", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074018, 3074017, 3074016], "chromosome": "Chromosome"}, "p.His207Arg": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.His207Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3073853, 3073852, 3073851], "chromosome": "Chromosome"}, "p.Gly91Arg": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Gly91Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074201, 3074200, 3074199], "chromosome": "Chromosome"}, "c.373dupT": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "c.373dupT", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074099], "chromosome": "Chromosome"}, "p.Tyr36Cys": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Tyr36Cys", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074366, 3074365, 3074364], "chromosome": "Chromosome"}, "p.His75Asn": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.His75Asn", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074249, 3074248, 3074247], "chromosome": "Chromosome"}, "p.Trp83*": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Trp83*", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074225, 3074224, 3074223], "chromosome": "Chromosome"}, "c.260delC": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "c.260delC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074212], "chromosome": "Chromosome"}, "p.Ser105Pro": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ser105Pro", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074159, 3074158, 3074157], "chromosome": "Chromosome"}, "p.Trp101Arg": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Trp101Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074171, 3074170, 3074169], "chromosome": "Chromosome"}, "p.Arg126Gln": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg126Gln", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3074096, 3074095, 3074094], "chromosome": "Chromosome"}}, "Rv2447c": {"p.Phe152Leu": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Phe152Leu", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747145, 2747144, 2747143], "chromosome": "Chromosome"}, "p.Arg91Trp": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg91Trp", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747328, 2747327, 2747326], "chromosome": "Chromosome"}, "p.Ala183Pro": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ala183Pro", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747052, 2747051, 2747050], "chromosome": "Chromosome"}, "p.Ser150Arg": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ser150Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747151, 2747150, 2747149], "chromosome": "Chromosome"}, "p.Leu56Val": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Leu56Val", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747433, 2747432, 2747431], "chromosome": "Chromosome"}, "p.Thr20Pro": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Thr20Pro", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747541, 2747540, 2747539], "chromosome": "Chromosome"}, "p.Ser150Gly": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ser150Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747151, 2747150, 2747149], "chromosome": "Chromosome"}, "p.Glu40Gln": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Glu40Gln", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747481, 2747480, 2747479], "chromosome": "Chromosome"}, "p.Phe152Ser": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Phe152Ser", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747145, 2747144, 2747143], "chromosome": "Chromosome"}, "p.Glu153Gly": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Glu153Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747142, 2747141, 2747140], "chromosome": "Chromosome"}, "p.Glu153Ala": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Glu153Ala", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747142, 2747141, 2747140], "chromosome": "Chromosome"}, "p.Arg49Pro": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg49Pro", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747454, 2747453, 2747452], "chromosome": "Chromosome"}, "p.Ile43Thr": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ile43Thr", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747472, 2747471, 2747470], "chromosome": "Chromosome"}, "p.Ser150Cys": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ser150Cys", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747151, 2747150, 2747149], "chromosome": "Chromosome"}, "p.Ile43Ser": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Ile43Ser", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747472, 2747471, 2747470], "chromosome": "Chromosome"}, "p.Asn73Ser": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Asn73Ser", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747382, 2747381, 2747380], "chromosome": "Chromosome"}, "p.Glu40Gly": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Glu40Gly", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747481, 2747480, 2747479], "chromosome": "Chromosome"}, "p.Arg49Trp": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Arg49Trp", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2747454, 2747453, 2747452], "chromosome": "Chromosome"}}, "Rv2245": {"p.Arg121Lys": {"annotations": [{"type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Arg121Lys", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2518475, 2518476, 2518477], "chromosome": "Chromosome"}, "p.Gly387Asp": {"annotations": [{"type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Gly387Asp", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2519273, 2519274, 2519275], "chromosome": "Chromosome"}, "p.Asp66Asn": {"annotations": [{"type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Asp66Asn", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2518310, 2518311, 2518312], "chromosome": "Chromosome"}, "p.Met77Ile": {"annotations": [{"type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Met77Ile", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2518343, 2518344, 2518345], "chromosome": "Chromosome"}}, "Rv2754c": {"c.-16C>T": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "c.-16C>T", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3067961], "chromosome": "Chromosome"}}, "Rv2780": {"c.133delA": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.133delA", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3086952], "chromosome": "Chromosome"}, "c.879_880dupGC": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.879_880dupGC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087698, 3087699], "chromosome": "Chromosome"}, "c.436_437dupGC": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.436_437dupGC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087255, 3087256], "chromosome": "Chromosome"}, "c.134_135dupTC": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.134_135dupTC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3086953, 3086954], "chromosome": "Chromosome"}, "c.992dupC": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.992dupC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087811], "chromosome": "Chromosome"}, "c.317_318insT": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.317_318insT", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087136, 3087137], "chromosome": "Chromosome"}, "c.464delG": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.464delG", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087283], "chromosome": "Chromosome"}, "c.130dupG": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.130dupG", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3086949], "chromosome": "Chromosome"}, "c.1107dupG": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.1107dupG", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087926], "chromosome": "Chromosome"}, "c.968_969dupAG": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.968_969dupAG", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087787, 3087788], "chromosome": "Chromosome"}, "c.839_843dupCGACC": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.839_843dupCGACC", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087658, 3087659, 3087660, 3087661, 3087662], "chromosome": "Chromosome"}, "c.897_898dupGA": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "c.897_898dupGA", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3087716, 3087717], "chromosome": "Chromosome"}}, "Rv3423c": {"p.Phe4Leu": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "p.Phe4Leu", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3841411, 3841410, 3841409], "chromosome": "Chromosome"}, "p.Met343Thr": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "p.Met343Thr", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3840394, 3840393, 3840392], "chromosome": "Chromosome"}, "p.Leu113Arg": {"annotations": [{"type": "drug_resistance", "drug": "cycloserine", "original_mutation": "p.Leu113Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [3841084, 3841083, 3841082], "chromosome": "Chromosome"}}, "Rv2671": {"p.Gly8Arg": {"annotations": [{"type": "drug_resistance", "drug": "para-aminosalicylic_acid", "original_mutation": "p.Gly8Arg", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [2986860, 2986861, 2986862], "chromosome": "Chromosome"}}, "Rv0643c": {"p.Gly98Asp": {"annotations": [{"type": "drug_resistance", "drug": "isoniazid", "original_mutation": "p.Gly98Asp", "confidence": "", "source": "tbdb", "comment": "Mutation from literature"}], "genome_positions": [737858, 737857, 737856], "chromosome": "Chromosome"}}} \ No newline at end of file diff --git a/db/tbdb.fasta.fai b/db/tbdb.fasta.fai deleted file mode 100644 index d80b5e4..0000000 --- a/db/tbdb.fasta.fai +++ /dev/null @@ -1 +0,0 @@ -Chromosome 4411532 77 60 61 diff --git a/db/tbdb.mask.bed b/db/tbdb.mask.bed index 4f324f7..96065fc 100644 --- a/db/tbdb.mask.bed +++ b/db/tbdb.mask.bed @@ -51,9 +51,7 @@ Chromosome 99162 99174 Chromosome 102100 102138 Chromosome 102140 102150 Chromosome 103743 103756 -Chromosome 103788 104164 -Chromosome 104317 104985 -Chromosome 104986 104987 +Chromosome 103788 104987 Chromosome 106207 106343 Chromosome 125830 125834 Chromosome 126259 126260 diff --git a/db/tbdb.rules.txt b/db/tbdb.rules.txt deleted file mode 100644 index 087889b..0000000 --- a/db/tbdb.rules.txt +++ /dev/null @@ -1,2 +0,0 @@ -Variant(gene_name=mmpL5,type=lof) inactivates_resistance Variant(gene_name=mmpR5) Loss of function variant found in mmpL5 which can abrogate the effect of genetically linked AwR and AwRI mmpR5 (Rv0678) resistance mutations. -Variant(gene_name=eis,type=lof) inactivates_resistance Variant(gene_name=eis) Loss of function variant found in eis which can abrogate the effect of genetically linked AwR and AwRI eis resistance mutations. diff --git a/db/tbdb.variables.json b/db/tbdb.variables.json index 7251043..475df6d 100644 --- a/db/tbdb.variables.json +++ b/db/tbdb.variables.json @@ -1,5 +1,5 @@ { - "db-schema-version": "1.0.0", + "db-schema-version": "1.1.0", "snpEff_db": "Mycobacterium_tuberculosis_h37rv", "drugs": [ "rifampicin", @@ -24,10 +24,14 @@ "tb-profiler-version": ">=6.0.0,<7.0.0", "version": { "name": "tbdb", - "commit": "72ef6fa", - "Author": "Jody Phelan ", - "Date": "Tue Jul 16 16:56:19 2024 +0100", - "db-schema-version": "1.0.0" + "repo": "git@github.com:jodyphelan/tbdb.git", + "branch": "tbdb", + "commit": "7066eb43", + "status": "clean", + "author": "Jody Phelan", + "date": "Fri Feb 14 09:41:10 2025 +0100", + "db-schema-version": "1.1.0", + "tb-profiler-version": ">=6.0.0,<7.0.0" }, "amplicon": false, "files": { @@ -39,7 +43,6 @@ "spoligotype_spacers": "tbdb.spoligotype_spacers.txt", "spoligotype_annotations": "tbdb.spoligotype_list.csv", "bedmask": "tbdb.mask.bed", - "barcode": "tbdb.barcode.bed", - "rules": "tbdb.rules.txt" + "barcode": "tbdb.barcode.bed" } } diff --git a/tb-profiler b/tb-profiler index 9aa9c62..eeaee79 100644 --- a/tb-profiler +++ b/tb-profiler @@ -35,6 +35,7 @@ discovered_plugins = { __softwarename__ = 'tbprofiler' __default_db_dir__ = f'{sys.base_prefix}/share/{__softwarename__}' +__compatible_db_schema_version__ = '1.0.0' @atexit.register def cleanup(): @@ -246,8 +247,6 @@ def main_update_tbdb(args): extra_args = [] - if os.path.isfile('rules.txt'): - extra_args.append("--rules rules.txt") if args.match_ref: extra_args.append("--match_ref %s" % os.path.abspath(args.match_ref)) @@ -260,8 +259,8 @@ def main_update_tbdb(args): def main_create_db(args): - version_string = json.load(open('variables.json'))['tb-profiler-version'] - tbp.check_db_version(version_string,tbp.__version__) + version_string = json.load(open('variables.json'))['db-schema-version'] + tbp.check_db_version(version_string,__compatible_db_schema_version__) if args.no_overwrite: dbs = pp.list_db(args.software_name) @@ -277,8 +276,6 @@ def main_create_db(args): } if args.barcode: extra_files["barcode"] = args.barcode - if args.rules: - extra_files["rules"] = args.rules with TempFilePrefix() as tmpfile: args.csv = tbp.reformat_variant_csv_file(args.csv,f'{tmpfile}.variants.csv') @@ -371,11 +368,11 @@ def main_batch(args): def main_list_db(args): - dbs = pp.list_db(args.software_name) + dbs = pp.list_db(args.db_dir) for db in dbs: if 'version' in db: - d = dict(**db['version'], location=f"{sys.base_prefix}/share/{args.software_name}/{db['version']['name']}") - sys.stdout.write("%(name)s\t%(commit)s\t%(Author)s\t%(Date)s\t%(location)s\n" % d) + d = dict(**db['version'], location=f"{args.db_dir}/{db['version']['name']}") + sys.stdout.write("%(name)s\t%(commit)s\t%(author)s\t%(date)s\t%(location)s\n" % d) @@ -587,7 +584,6 @@ parser_sub.add_argument('--spoligotypes',default="spoligotype_spacers.txt",type= parser_sub.add_argument('--spoligotype_annotations','--spoligotype-annotations',default="spoligotype_list.csv") parser_sub.add_argument('--barcode',default="barcode.bed",type=str,help='A bed file containing lineage barcode SNPs') parser_sub.add_argument('--bedmask',default="mask.bed",type=str,help='A bed file containing a list of low-complexity regions') -parser_sub.add_argument('--rules',type=str,default="rules.txt",help='A file containing python rules') parser_sub.add_argument('--amplicon_primers','--amplicon-primers',type=str,help='A file containing a list of amplicon primers') parser_sub.add_argument('--match_ref','--match-ref',type=str,help='Match the chromosome name to the given fasta file') parser_sub.add_argument('--custom',action="store_true",help='Tells the script this is a custom database, this is used to alter the generation of the version definition') @@ -639,6 +635,7 @@ parser_sub.add_argument('--args',type=str, help='Arguments to use with tb-profil parser_sub.add_argument('--jobs','-j',default=1,help='Threads to use',type=int) parser_sub.add_argument('--threads_per_job','--threads-per-job','-t',default=1,help='Threads to use',type=int) parser_sub.add_argument('--dir','-d',default=".",help='Storage directory') +parser_sub.add_argument('--db_dir',type=os.path.abspath,default=__default_db_dir__,help='Database directory') parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS) parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".") parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__) @@ -650,6 +647,7 @@ parser_sub = subparsers.add_parser('list_db', help='List loaded databases', form parser_sub.add_argument('--dir','-d',default=".",help='Storage directory') parser_sub.add_argument('--no_clean','--no-clean', action='store_true',help=argparse.SUPPRESS) parser_sub.add_argument('--temp',help="Temp firectory to process all files",type=str,default=".") +parser_sub.add_argument('--db_dir',type=os.path.abspath,default=__default_db_dir__,help='Database directory') parser_sub.add_argument('--version', action='version', version="tb-profiler version %s" % tbp.__version__) parser_sub.add_argument('--logging',type=str.upper,default="INFO",choices=["DEBUG","INFO","WARNING","ERROR","CRITICAL"],help='Logging level') parser_sub.add_argument('--debug',action='store_true',help=argparse.SUPPRESS) diff --git a/tbprofiler/reformat.py b/tbprofiler/reformat.py index 9d78422..6e679a6 100644 --- a/tbprofiler/reformat.py +++ b/tbprofiler/reformat.py @@ -3,7 +3,7 @@ from typing import List, Tuple , Union, Optional from .utils import get_gene2drugs import argparse -from pathogenprofiler.utils import shared_dict +from pathogenprofiler.utils import shared_dict, get_software_used def get_main_lineage(lineages: List[Lineage],max_node_skip: int = 1) -> Tuple[str, str]: """ @@ -206,7 +206,7 @@ def create_lineage_result( pipeline = Pipeline( software_version=args.version, db_version=args.conf['version'], - software=[{'process':k,'software':v} for k,v in shared_dict.items()] + software=get_software_used() ) data = { 'id':args.prefix, @@ -233,7 +233,7 @@ def create_resistance_result( pipeline = Pipeline( software_version=args.version, db_version=args.conf['version'], - software=[{'process':k,'software':v} for k,v in shared_dict.items()] + software=get_software_used() ) if hasattr(qc, 'missing_positions'): qc.missing_positions = filter_missing_positions(qc.missing_positions) diff --git a/tbprofiler/utils.py b/tbprofiler/utils.py index e4cdd23..4066312 100644 --- a/tbprofiler/utils.py +++ b/tbprofiler/utils.py @@ -4,6 +4,8 @@ import csv import logging import re +from packaging.version import Version + def process_tb_profiler_args(args: argparse.Namespace) -> None: if args.snp_dist: @@ -93,17 +95,11 @@ def reformat_variant_csv_file(files: list, outfile: str) -> str: return outfile -def check_db_version(db_version: str, tbprofiler_version: str) -> None: - for d in db_version.split(","): - r = re.search('([<>=]+)(.*)',d) - if r==None: - logging.error(f"Invalid version string: {d}") - quit(1) - - d = f"{r.group(1)} '{r.group(2)}'" - if eval(f"'{tbprofiler_version}' {d}")==False: - if ">" in d: - logging.error(f"Your version of tb-profiler ({tbprofiler_version}) is too old to use this version of the database. Please update tb-profiler to {db_version}") - else: - logging.error(f"Your version of tb-profiler ({tbprofiler_version}) is too new to use this version of the database. Please update the database to {db_version}") - quit(1) \ No newline at end of file +def check_db_version(db_current_version_str: str, compatible_schema_version_str: str): + db_current_version = Version(db_current_version_str) + compatible_schema_version = Version(compatible_schema_version_str) + logging.debug(f"Database version: {db_current_version}") + logging.debug(f"Compatible schema version: {compatible_schema_version}") + if db_current_version.major != compatible_schema_version.major: + logging.error(f"Latest database schema version {db_current_version_str} is not compatible with this version of tb-profiler (requires {compatible_schema_version.major}.x.x). Please make sure you are using the latest software and database versions.") + quit(1) \ No newline at end of file diff --git a/tests/run_test.py b/tests/run_test.py index 4c341a3..d982ddf 100644 --- a/tests/run_test.py +++ b/tests/run_test.py @@ -13,15 +13,6 @@ if not os.path.isdir("tb-profiler-test-data"): run_cmd("git clone https://github.com/jodyphelan/tb-profiler-test-data.git") -# por5_dr_variants = [ -# ('rpoB', 'p.Ser450Leu'), -# ('fabG1', 'c.-15C>T'), -# ('inhA', 'p.Ile194Thr'), -# ('pncA', 'p.Val125Gly'), -# ('embB', 'p.Met306Val'), -# ('embB', 'p.Met423Thr'), -# ('gid', 'p.Ala80Pro') -# ] por5_dr_variants = [ ('rpoB', 'p.Ser450Leu'), @@ -59,8 +50,8 @@ def test_vcf(): check_assertations("results/por5_vcf.results.json") def test_nanopore(): - run_cmd(f"tb-profiler profile --db {db} -1 tb-profiler-test-data/por5A.nanopore_reduced.fastq.gz --platform nanopore -p por5A_illumina_nanopore -t 4 --af '0.5,0.7' --depth '0,5' --txt --csv --docx") - check_assertations("results/por5A_illumina_nanopore.results.json") + run_cmd(f"tb-profiler profile --db {db} -1 tb-profiler-test-data/por5A.nanopore_reduced.fastq.gz --platform nanopore -p por5A_nanopore -t 4 --caller bcftools --af '0.5,0.7' --depth '0,5' --txt --csv --docx") + check_assertations("results/por5A_nanopore.results.json") def test_fasta(): run_cmd(f"tb-profiler profile --db {db} -f tb-profiler-test-data/por5A1.fasta -p por5A_fasta --txt --csv --docx")