Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

update resistance gene bed #46

Merged
merged 5 commits into from
Nov 5, 2024
Merged

update resistance gene bed #46

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
4b3f6c0
update resistance gene bed
taranewman Oct 23, 2024
1d08501
use geonome positions from tbdb bed
taranewman Oct 24, 2024
d6c555a
add drug column from tbdb bed
taranewman Oct 24, 2024
11811ea
add resistance gene coverage per drug
taranewman Oct 25, 2024
5e12b89
Update make_resistance_genes_bed.py
taranewman Oct 25, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
108 changes: 73 additions & 35 deletions assets/resistance_genes.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,35 +1,73 @@
Chromosome 5239 7267 gyrB 0 +
Chromosome 7301 9818 gyrA 0 +
Chromosome 490782 491793 fgd1 0 +
Chromosome 759806 763325 rpoB 0 +
Chromosome 763369 767320 rpoC 0 +
Chromosome 778989 779487 mmpR5 0 +
Chromosome 781559 781934 rpsL 0 +
Chromosome 800808 801462 rplC 0 +
Chromosome 1416180 1417347 embR 0 -
Chromosome 1471845 1473382 rrs 0 +
Chromosome 1473657 1476795 rrl 0 +
Chromosome 1673439 1674183 fabG1 0 +
Chromosome 1674201 1675011 inhA 0 +
Chromosome 1833541 1834987 rpsA 0 +
Chromosome 1917939 1918746 tlyA 0 +
Chromosome 2153888 2156111 katG 0 -
Chromosome 2288680 2289241 pncA 0 -
Chromosome 2518114 2519365 kasA 0 +
Chromosome 2714123 2715332 eis 0 -
Chromosome 2726192 2726780 ahpC 0 +
Chromosome 2746134 2747598 folC 0 -
Chromosome 2986838 2987615 ribD 0 +
Chromosome 3067192 3067945 thyX 0 -
Chromosome 3073679 3074471 thyA 0 -
Chromosome 3086819 3087935 ald 0 +
Chromosome 3640542 3641538 fbiA 0 +
Chromosome 3840193 3841420 alr 0 -
Chromosome 3986843 3987299 ddn 0 +
Chromosome 4043861 4044281 panD 0 -
Chromosome 4239862 4243147 embC 0 +
Chromosome 4243232 4246517 embA 0 +
Chromosome 4246513 4249810 embB 0 +
Chromosome 4326003 4327473 ethA 0 -
Chromosome 4327548 4328199 ethR 0 +
Chromosome 4407527 4408202 gid 0 -
Chromosome 0 1524 dnaA 0 + isoniazid
Chromosome 4932 7267 gyrB 0 + levofloxacin,moxifloxacin
Chromosome 7067 9818 gyrA 0 + levofloxacin,moxifloxacin
Chromosome 13132 13911 Rv0010c 0 - isoniazid
Chromosome 490544 491793 fgd1 0 + pretomanid,delamanid,clofazimine
Chromosome 574478 576790 mshA 0 + isoniazid,ethionamide
Chromosome 619499 620865 ccsA 0 + kanamycin,capreomycin,amikacin
Chromosome 656009 657739 Rv0565c 0 - ethionamide
Chromosome 731679 732406 hadA 0 + isoniazid
Chromosome 733852 734970 nusG 0 + rifampicin
Chromosome 737267 738349 mmaA3 0 - isoniazid
Chromosome 759341 763325 rpoB 0 + rifampicin
Chromosome 763126 767320 rpoC 0 + rifampicin
Chromosome 775585 778680 mmpL5 0 - bedaquiline,clofazimine
Chromosome 778476 779624 mmpS5 0 - bedaquiline,clofazimine
Chromosome 778789 779487 mmpR5 0 + bedaquiline,clofazimine
Chromosome 781125 781934 rpsL 0 + streptomycin
Chromosome 800105 801462 rplC 0 + linezolid
Chromosome 1253073 1254783 Rv1129c 0 - levofloxacin,moxifloxacin,isoniazid,rifampicin
Chromosome 1302605 1305501 fbiC 0 + pretomanid,delamanid,clofazimine
Chromosome 1364161 1365186 sigE 0 + pyrazinamide
Chromosome 1406080 1407604 Rv1258c 0 - streptomycin,pyrazinamide,isoniazid
Chromosome 1416180 1418048 embR 0 - ethambutol
Chromosome 1460801 1461290 atpE 0 + bedaquiline
Chromosome 1471497 1473382 rrs 0 + kanamycin,capreomycin,streptomycin,amikacin
Chromosome 1473407 1476795 rrl 0 + capreomycin,linezolid
Chromosome 1673147 1675011 inhA 0 + isoniazid,ethionamide
Chromosome 1833246 1834987 rpsA 0 + pyrazinamide
Chromosome 1853357 1854388 tsnR 0 + linezolid
Chromosome 1917505 1918746 tlyA 0 + capreomycin
Chromosome 2062808 2065010 bacA 0 - kanamycin,capreomycin,streptomycin,amikacin
Chromosome 2101650 2103337 ndh 0 - isoniazid,delamanid,ethionamide
Chromosome 2153888 2156842 katG 0 - isoniazid
Chromosome 2167648 2170934 PPE35 0 - pyrazinamide
Chromosome 2221718 2223825 Rv1979c 0 - bedaquiline,clofazimine
Chromosome 2288680 2290323 pncA 0 - pyrazinamide
Chromosome 2517914 2519365 kasA 0 + isoniazid
Chromosome 2714123 2715832 eis 0 - kanamycin,amikacin
Chromosome 2725898 2726780 ahpC 0 + isoniazid
Chromosome 2746134 2747798 folC 0 - para-aminosalicylic_acid
Chromosome 2782365 2786169 Rv2477c 0 - kanamycin,levofloxacin,moxifloxacin,streptomycin,rifampicin,ethambutol,amikacin
Chromosome 2859299 2860640 pepQ 0 - bedaquiline,clofazimine
Chromosome 2986638 2987615 ribD 0 + para-aminosalicylic_acid
Chromosome 2995771 2996737 Rv2680 0 + capreomycin
Chromosome 2996538 2998055 Rv2681 0 + capreomycin
Chromosome 3064514 3067372 Rv2752c 0 - levofloxacin,moxifloxacin,isoniazid,rifampicin,ethambutol
Chromosome 3067192 3068161 thyX 0 - para-aminosalicylic_acid
Chromosome 3073679 3074671 thyA 0 - para-aminosalicylic_acid
Chromosome 3086619 3087935 ald 0 + cycloserine
Chromosome 3338867 3339762 fbiD 0 + pretomanid,delamanid,clofazimine
Chromosome 3448252 3449991 Rv3083 0 + ethionamide
Chromosome 3568400 3569280 whiB7 0 - kanamycin,amikacin,streptomycin
Chromosome 3611958 3613847 Rv3236c 0 - pyrazinamide
Chromosome 3623158 3625110 lpqB 0 - rifampicin,bedaquiline
Chromosome 3624909 3626860 mtrB 0 - rifampicin,bedaquiline
Chromosome 3626662 3627924 mtrA 0 - rifampicin,bedaquiline
Chromosome 3640206 3641538 fbiA 0 + pretomanid,delamanid,clofazimine
Chromosome 3641334 3642881 fbiB 0 + pretomanid,delamanid,clofazimine
Chromosome 3840193 3841620 alr 0 - cycloserine
Chromosome 3877463 3879240 rpoA 0 - rifampicin
Chromosome 3986611 3987299 ddn 0 + pretomanid,delamanid
Chromosome 4038157 4041013 clpC1 0 - pyrazinamide
Chromosome 4043861 4046428 panD 0 - pyrazinamide
Chromosome 4138201 4140002 glpK 0 - levofloxacin,moxifloxacin,isoniazid,streptomycin,rifampicin,ethambutol
Chromosome 4237682 4243147 embC 0 + ethambutol
Chromosome 4242946 4246517 embA 0 + ethambutol
Chromosome 4246313 4249810 embB 0 + ethambutol
Chromosome 4266952 4269124 aftB 0 - ethambutol
Chromosome 4268924 4270084 ubiA 0 - ethambutol
Chromosome 4326003 4330174 ethA 0 - ethionamide
Chromosome 4327327 4328199 ethR 0 + ethionamide
Chromosome 4338170 4338961 whiB6 0 - kanamycin,capreomycin,amikacin
Chromosome 4407527 4408481 gid 0 - streptomycin
73 changes: 73 additions & 0 deletions assets/tbdb.bed
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,73 @@
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 656010 657739 Rv0565c Rv0565c ethionamide
Chromosome 731680 732406 Rv0635 hadA isoniazid
Chromosome 733853 734970 Rv0639 nusG rifampicin
Chromosome 737268 738349 Rv0643c mmaA3 isoniazid
Chromosome 759342 763325 Rv0667 rpoB rifampicin
Chromosome 763127 767320 Rv0668 rpoC rifampicin
Chromosome 775586 778680 Rv0676c mmpL5 bedaquiline,clofazimine
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 1364162 1365186 Rv1221 sigE pyrazinamide
Chromosome 1406081 1407604 Rv1258c Rv1258c streptomycin,pyrazinamide,isoniazid
Chromosome 1416181 1418048 Rv1267c embR ethambutol
Chromosome 1460802 1461290 Rv1305 atpE bedaquiline
Chromosome 1471498 1473382 EBG00000313325 rrs kanamycin,capreomycin,streptomycin,amikacin
Chromosome 1473408 1476795 EBG00000313339 rrl capreomycin,linezolid
Chromosome 1673148 1675011 Rv1484 inhA isoniazid,ethionamide
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 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 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 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 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 3448253 3449991 Rv3083 Rv3083 ethionamide
Chromosome 3568401 3569280 Rv3197A whiB7 kanamycin,amikacin,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 3840194 3841620 Rv3423c alr cycloserine
Chromosome 3877464 3879240 Rv3457c rpoA rifampicin
Chromosome 3986612 3987299 Rv3547 ddn pretomanid,delamanid
Chromosome 4038158 4041013 Rv3596c clpC1 pyrazinamide
Chromosome 4043862 4046428 Rv3601c panD pyrazinamide
Chromosome 4138202 4140002 Rv3696c glpK levofloxacin,moxifloxacin,isoniazid,streptomycin,rifampicin,ethambutol
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 kanamycin,capreomycin,amikacin
Chromosome 4407528 4408481 Rv3919c gid streptomycin
Loading
Loading