Skip to content

Commit

Permalink
Merge pull request #332 from jodyphelan/dev
Browse files Browse the repository at this point in the history 
Dev
  • Loading branch information
@jodyphelan
jodyphelan committed Mar 17, 2024
2 parents 8b09761 + d10739f commit 5779a97
Show file tree
Hide file tree
Showing 27 changed files with 7,616 additions and 275,767 deletions.
334 changes: 191 additions & 143 deletions conda/linux-latest.txt
View file

Large diffs are not rendered by default.

10 changes: 10 additions & 0 deletions db/tbdb.barcode.bed
View file
Original file line number Diff line number Diff line change
Expand Up @@ -259,6 +259,7 @@ Chromosome 506385 506386 lineage4.4.1.1 C Euro-American S;Orphans None
Chromosome 511349 511350 lineage5.3 A West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 514244 514245 lineage4.1.1 T Euro-American (X-type) X1;X2;X3 None
Chromosome 522052 522053 lineage2.1 A East-Asian (non-Beijing) None None
Chromosome 526895 526896 M.canetti C M.canetti None None
Chromosome 528780 528781 lineage1.2.1.2 A Indo-Oceanic NA RD239
Chromosome 529362 529363 lineage1.1.1 T Indo-Oceanic EAI4;EAI5 RD239
Chromosome 533327 533328 La2 A M.caprae None None
Expand Down Expand Up @@ -330,6 +331,7 @@ Chromosome 703721 703722 lineage4.1.1.3.1 G Euro-American (X-type) X1;X3 RD193
Chromosome 705061 705062 lineage4.4.1.1 C Euro-American S;Orphans None
Chromosome 705569 705570 lineage1.1 T Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239
Chromosome 705594 705595 lineage4.3.2 T Euro-American (LAM) LAM3 None
Chromosome 707485 707486 M.canetti C M.canetti None None
Chromosome 709492 709493 lineage4.8.3 T Euro-American (mainly T) T1;T2;T3;T5 RD219
Chromosome 709656 709657 lineage5.1.4 C West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 711154 711155 lineage1.1.2 A Indo-Oceanic EAI3;EAI5 RD239
Expand All @@ -352,6 +354,7 @@ Chromosome 748922 748923 lineage4.8.3 T Euro-American (mainly T) T1;T2;T3;T5 RD2
Chromosome 753087 753088 lineage4.4 T Euro-American S;T None
Chromosome 756567 756568 lineage6.2 A West-Africa 2 AFRI_1 RD702
Chromosome 758121 758122 lineage4.6.3 T Euro-American T;LAM None
Chromosome 764151 764152 M.canetti T M.canetti None None
Chromosome 771653 771654 lineage5.3 G West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 771722 771723 lineage6.3.2 A West-Africa 2 AFRI_1 RD702
Chromosome 772739 772740 La1.7 T M.bovis None None
Expand Down Expand Up @@ -609,6 +612,7 @@ Chromosome 1560776 1560777 lineage5.1.3 A West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 1560911 1560912 lineage1 A Indo-Oceanic EAI RD239
Chromosome 1561244 1561245 lineage7 T Lineage 7 None None
Chromosome 1564798 1564799 lineage4.1.3 T Euro-American T;X;H None
Chromosome 1565424 1565425 M.canetti A M.canetti None None
Chromosome 1565565 1565566 lineage2.2.2 T East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207
Chromosome 1567984 1567985 lineage1.2.1.2 G Indo-Oceanic NA RD239
Chromosome 1568017 1568018 lineage4.2 T Euro-American H;T;LAM None
Expand Down Expand Up @@ -725,6 +729,7 @@ Chromosome 2024412 2024413 lineage6.3.1 T West-Africa 2 AFRI_1 RD702
Chromosome 2027616 2027617 La1.2.BCG A M.bovis BCG None
Chromosome 2033747 2033748 lineage4.6.1 C Euro-American (Uganda) T2 RD724
Chromosome 2033889 2033890 lineage4.4.1 T Euro-American (S-type) S;T None
Chromosome 2043079 2043080 M.canetti G M.canetti None None
Chromosome 2053681 2053682 lineage4.3 T Euro-American (LAM) mainly-LAM None
Chromosome 2054804 2054805 lineage4.1.1.3 A Euro-American (X-type) X1;X3 RD193
Chromosome 2058446 2058447 lineage4.6.1.2 A Euro-American T2 RD724
Expand Down Expand Up @@ -933,6 +938,7 @@ Chromosome 3147315 3147316 lineage1.2.2.2 A Indo-Oceanic NA RD239
Chromosome 3147375 3147376 lineage4.4.1 A Euro-American (S-type) S;T None
Chromosome 3147510 3147511 lineage2.2.2 G East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207
Chromosome 3147741 3147742 lineage4.1.2 G Euro-American T;H None
Chromosome 3148166 3148167 M.canetti G M.canetti None None
Chromosome 3153182 3153183 lineage6.3 G West-Africa 2 AFRI_1 RD702
Chromosome 3168966 3168967 lineage4.8 A Euro-American (mainly T) T1;T2;T3;T5 RD219
Chromosome 3170459 3170460 lineage4.6 T Euro-American T;LAM None
Expand All @@ -950,6 +956,7 @@ Chromosome 3253570 3253571 lineage4.1.1.3.1 T Euro-American (X-type) X1;X3 RD193
Chromosome 3259271 3259272 lineage4.2.2.1 C Euro-American LAM7-TUR None
Chromosome 3270288 3270289 lineage4.7 A Euro-American (mainly T) T1;T5 None
Chromosome 3285944 3285945 lineage4.3.4.1 G Euro-American (LAM) LAM1;LAM2 RD174
Chromosome 3287787 3287788 M.canetti G M.canetti None None
Chromosome 3293314 3293315 lineage4.6.2.1 T Euro-American T3 RD726
Chromosome 3323664 3323665 lineage1.2.2.1 A Indo-Oceanic NA RD239
Chromosome 3332625 3332626 lineage4.6.1.2 T Euro-American T2 RD724
Expand All @@ -963,6 +970,7 @@ Chromosome 3354624 3354625 lineage4.6.2.2 A Euro-American (Cameroon) LAM10-CAM R
Chromosome 3360031 3360032 lineage4.3.1.1 A Euro-American (LAM) LAM9 None
Chromosome 3360151 3360152 lineage4.6.2.2 A Euro-American (Cameroon) LAM10-CAM RD726
Chromosome 3363400 3363401 lineage6.3.3 A West-Africa 2 AFRI_1 RD702
Chromosome 3367416 3367417 M.canetti A M.canetti None None
Chromosome 3367764 3367765 lineage4.9 G Euro-American (H37Rv-like) T1 None
Chromosome 3368283 3368284 lineage5.1.1 T West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 3368414 3368415 lineage6.2.2 A West-Africa 2 AFRI_1 RD702
Expand Down Expand Up @@ -1027,6 +1035,7 @@ Chromosome 3886877 3886878 lineage4.4.2 C Euro-American T1;T2 None
Chromosome 3893138 3893139 lineage5.1.4 A West-Africa 1 AFRI_2;AFRI_3 RD711
Chromosome 3918066 3918067 lineage6.1.1 C West-Africa 2 AFRI_1 RD702
Chromosome 3955403 3955404 lineage6.1.1 A West-Africa 2 AFRI_1 RD702
Chromosome 4000017 4000018 M.canetti G M.canetti None None
Chromosome 4001040 4001041 lineage6.2.1 A West-Africa 2 AFRI_1 RD702
Chromosome 4004035 4004036 lineage4.4 T Euro-American S;T None
Chromosome 4024367 4024368 lineage1.2.1.2 T Indo-Oceanic NA RD239
Expand Down Expand Up @@ -1063,6 +1072,7 @@ Chromosome 4200992 4200993 lineage1.2.2.2 G Indo-Oceanic NA RD239
Chromosome 4204695 4204696 La1.8.2 A M.bovis None None
Chromosome 4228100 4228101 lineage4.1.3 T Euro-American T;X;H None
Chromosome 4229086 4229087 lineage4.1.1.3 T Euro-American (X-type) X1;X3 RD193
Chromosome 4231381 4231382 M.canetti G M.canetti None None
Chromosome 4236890 4236891 lineage6 A West-Africa 2 AFRI_1 RD702
Chromosome 4236902 4236903 lineage4.6.4 A Euro-American T;LAM None
Chromosome 4237382 4237383 lineage1.2.1.2 A Indo-Oceanic NA RD239
Expand Down
131 changes: 73 additions & 58 deletions db/tbdb.bed
View file
Original file line number Diff line number Diff line change
@@ -1,58 +1,73 @@
Chromosome 5040 7467 Rv0005 gyrB fluoroquinolones,moxifloxacin,levofloxacin,ciprofloxacin,ofloxacin
Chromosome 7102 10018 Rv0006 gyrA fluoroquinolones,moxifloxacin,levofloxacin,ciprofloxacin,ofloxacin
Chromosome 490583 491993 Rv0407 fgd1 delamanid
Chromosome 575148 576990 Rv0486 mshA ethionamide,isoniazid
Chromosome 619691 621065 Rv0529 ccsA capreomycin,amikacin
Chromosome 759607 763525 Rv0667 rpoB rifampicin
Chromosome 763170 767520 Rv0668 rpoC rifampicin
Chromosome 775386 778680 Rv0676c mmpL5 clofazimine,bedaquiline
Chromosome 778277 779105 Rv0677c mmpS5 clofazimine,bedaquiline
Chromosome 778790 779687 Rv0678 mmpR5 clofazimine,bedaquiline
Chromosome 781360 782134 Rv0682 rpsL streptomycin
Chromosome 800609 801662 Rv0701 rplC linezolid
Chromosome 1302731 1305701 Rv1173 fbiC delamanid
Chromosome 1405881 1407540 Rv1258c Rv1258c streptomycin,pyrazinamide,isoniazid
Chromosome 1415981 1417547 Rv1267c embR ethambutol
Chromosome 1460845 1461490 Rv1305 atpE bedaquiline
Chromosome 1471646 1473582 EBG00000313325 rrs linezolid,kanamycin,capreomycin,amikacin,aminoglycosides,streptomycin
Chromosome 1473458 1476995 EBG00000313339 rrl linezolid
Chromosome 1673148 1674383 Rv1483 fabG1 ethionamide,isoniazid
Chromosome 1673848 1675211 Rv1484 inhA ethionamide,isoniazid
Chromosome 1833342 1835187 Rv1630 rpsA pyrazinamide
Chromosome 1917740 1918946 Rv1694 tlyA capreomycin
Chromosome 2101451 2103242 Rv1854c ndh ethionamide,isoniazid
Chromosome 2153689 2156570 Rv1908c katG isoniazid
Chromosome 2167449 2170812 Rv1918c PPE35 pyrazinamide
Chromosome 2221519 2223364 Rv1979c Rv1979c clofazimine,bedaquiline
Chromosome 2288481 2290323 Rv2043c pncA pyrazinamide
Chromosome 2517915 2519565 Rv2245 kasA isoniazid
Chromosome 2713924 2715586 Rv2416c eis kanamycin,amikacin
Chromosome 2725912 2726980 Rv2428 ahpC isoniazid
Chromosome 2745935 2747798 Rv2447c folC para-aminosalicylic_acid
Chromosome 2859100 2860618 Rv2535c pepQ clofazimine,bedaquiline
Chromosome 2986639 2987815 Rv2671 ribD para-aminosalicylic_acid
Chromosome 3064315 3066391 Rv2752c Rv2752c rifampicin,isoniazid
Chromosome 3066993 3068161 Rv2754c thyX para-aminosalicylic_acid
Chromosome 3073480 3074671 Rv2764c thyA para-aminosalicylic_acid
Chromosome 3086620 3088135 Rv2780 ald cycloserine
Chromosome 3338918 3339962 Rv2983 fbiD delamanid
Chromosome 3448304 3450191 Rv3083 Rv3083 ethionamide
Chromosome 3473807 3475577 Rv3106 fprA capreomycin,amikacin
Chromosome 3568201 3568879 Rv3197A whiB7 streptomycin,kanamycin,amikacin
Chromosome 3611759 3613316 Rv3236c Rv3236c pyrazinamide
Chromosome 3640343 3641738 Rv3261 fbiA delamanid
Chromosome 3641335 3643081 Rv3262 fbiB delamanid
Chromosome 3839994 3841620 Rv3423c alr cycloserine
Chromosome 3877264 3878707 Rv3457c rpoA rifampicin
Chromosome 3986644 3987499 Rv3547 ddn delamanid
Chromosome 4037958 4040904 Rv3596c clpC1 pyrazinamide
Chromosome 4043662 4044481 Rv3601c panD pyrazinamide
Chromosome 4239663 4243347 Rv3793 embC ethambutol
Chromosome 4243004 4246717 Rv3794 embA ethambutol
Chromosome 4246314 4250010 Rv3795 embB ethambutol
Chromosome 4266753 4269036 Rv3805c aftB capreomycin,amikacin
Chromosome 4268725 4270033 Rv3806c ubiA ethambutol
Chromosome 4325804 4330174 Rv3854c ethA ethionamide
Chromosome 4327349 4328399 Rv3855 ethR ethionamide
Chromosome 4337971 4338721 Rv3862c whiB6 streptomycin,capreomycin,amikacin
Chromosome 4407328 4408476 Rv3919c gid streptomycin
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 clofazimine,pretomanid,delamanid
Chromosome 574479 576790 Rv0486 mshA ethionamide,isoniazid
Chromosome 619500 620865 Rv0529 ccsA capreomycin,amikacin,kanamycin
Chromosome 656010 657739 Rv0565c Rv0565c ethionamide
Chromosome 731680 732406 Rv0635 hadA isoniazid
Chromosome 733853 734970 Rv0639 nusG rifampicin
Chromosome 759342 763325 Rv0667 rpoB rifampicin
Chromosome 763127 767320 Rv0668 rpoC rifampicin
Chromosome 775586 778680 Rv0676c mmpL5 clofazimine,bedaquiline
Chromosome 778477 779624 Rv0677c mmpS5 clofazimine,bedaquiline
Chromosome 778790 779487 Rv0678 mmpR5 clofazimine,bedaquiline
Chromosome 781126 781934 Rv0682 rpsL streptomycin
Chromosome 800106 801462 Rv0701 rplC linezolid
Chromosome 1253074 1254783 Rv1129c Rv1129c moxifloxacin,levofloxacin,rifampicin,isoniazid
Chromosome 1302606 1305501 Rv1173 fbiC clofazimine,pretomanid,delamanid
Chromosome 1364162 1365186 Rv1221 sigE pyrazinamide
Chromosome 1406081 1407604 Rv1258c Rv1258c streptomycin,isoniazid,pyrazinamide
Chromosome 1416181 1418048 Rv1267c embR ethambutol
Chromosome 1460802 1461290 Rv1305 atpE bedaquiline
Chromosome 1471498 1473382 EBG00000313325 rrs streptomycin,kanamycin,capreomycin,amikacin
Chromosome 1473408 1476795 EBG00000313339 rrl capreomycin,linezolid
Chromosome 1673148 1674183 Rv1483 fabG1 ethionamide,isoniazid
Chromosome 1673189 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 streptomycin,kanamycin,capreomycin,amikacin
Chromosome 2101651 2103337 Rv1854c ndh ethionamide,delamanid,isoniazid
Chromosome 2153889 2156842 Rv1908c katG isoniazid
Chromosome 2167649 2170934 Rv1918c PPE35 pyrazinamide
Chromosome 2221719 2223825 Rv1979c Rv1979c clofazimine,bedaquiline
Chromosome 2288681 2290323 Rv2043c pncA pyrazinamide
Chromosome 2517915 2519365 Rv2245 kasA isoniazid
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 ethambutol,moxifloxacin,streptomycin,levofloxacin,kanamycin,rifampicin,amikacin
Chromosome 2859300 2860640 Rv2535c pepQ clofazimine,bedaquiline
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 ethambutol,moxifloxacin,levofloxacin,rifampicin,isoniazid
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 clofazimine,pretomanid,delamanid
Chromosome 3448253 3449991 Rv3083 Rv3083 ethionamide
Chromosome 3568401 3569280 Rv3197A whiB7 streptomycin,amikacin,kanamycin
Chromosome 3611959 3613847 Rv3236c Rv3236c pyrazinamide
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,pretomanid,delamanid
Chromosome 3641335 3642881 Rv3262 fbiB clofazimine,pretomanid,delamanid
Chromosome 3840194 3841620 Rv3423c alr cycloserine
Chromosome 3877464 3879240 Rv3457c rpoA rifampicin
Chromosome 3986612 3987299 Rv3547 ddn delamanid,pretomanid
Chromosome 4038158 4041013 Rv3596c clpC1 pyrazinamide
Chromosome 4043862 4046428 Rv3601c panD pyrazinamide
Chromosome 4138202 4140002 Rv3696c glpK ethambutol,moxifloxacin,streptomycin,levofloxacin,rifampicin,isoniazid
Chromosome 4237683 4243147 Rv3793 embC ethambutol
Chromosome 4242947 4246517 Rv3794 embA ethambutol
Chromosome 4246314 4249810 Rv3795 embB ethambutol
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 capreomycin,amikacin,kanamycin
Chromosome 4407528 4408481 Rv3919c gid streptomycin
2 changes: 2 additions & 0 deletions db/tbdb.dict
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
@HD VN:1.6
@SQ SN:Chromosome LN:4411532 M5:57b12ff2773c5fd3a0f879972f176e50 UR:file:/Users/jody/github/TBProfiler/db/tbdb.fasta
Loading

0 comments on commit 5779a97

Please sign in to comment.