update resistance gene bed (#46)

* update resistance gene bed

* use geonome  positions from tbdb bed

* add drug column from tbdb bed

* add resistance gene coverage per drug

* Update make_resistance_genes_bed.py

assets/resistance_genes.bed

@@ -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

assets/tbdb.bed

@@ -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