Add methbat map for filtering and annotation

[inemesb]

Description

This PR adds a mapping file that can be used to filter and annotate the methbat output based on regions, independent of the cpg_label column. This would create an output file that is better for Scout implementation.
Since the cpg_label would no longer be used for parsing, I have also included more information from the NanoImprint repo in this column for both the regions file and methbat background file.

Added

• methbat mapping file for filtering and annotation

Changed

• cpg_label in regions file to contain more information from nanoimprint
• cpg_label in background file to contain more information from nanoimprint

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[inemesb]

I will add some more information on creating the mapping file in this PR draft, hopefully it will be useful for later documentation.

ANNOTATION NOTES

• The mapping file was based on the original nallo/region/grch38_methbat_promoters_nanoimprint.tsv, adding three columns to the regions: hgnc_symbol, hgnc_id, and region_type (promoter or nanoimprint)
• The hgnc_symbol was annotated based on the gene for each promoter region or based on the gene annotations from nanoimprint, then corresponding HGNC IDs were found, and region_type was based on the source of each region.
• Nanoimprint regions GNAS-NESP GNASA/B GNASXL were all annotated with the same symbol GNAS and ID 4392.
• The two MEG3 regions from nanoimprint were also given the same symbol and ID 14575.

FILTERING NOTES

• All rows with hgnc ID not found were removed from the map.
• For redundant genes found in both nanoimprint and promoter regions, promoter region rows were removed, as nanoimprint regions were prioritized due to having more evidence of ASM. An exception is the IGF2 promoter window, since the nanoimprint region is really between IGF2 and H19.
• This filtering removed the following 143 regions which are present in nallo/region/grch38_methbat_promoters_nanoimprint.tsv but not in the map:

chrom	start	end	hgnc_symbol	hgnc_id	region_type
chr6	144008260	144009259	PLAGL1	9046	promoter
chr7	50782897	50783896	GRB10	4564	promoter
chr7	130491085	130492084	MEST	7028	promoter
chr15	23647868	23648867	MAGEL2	6814	promoter
chr15	24953987	24954986	SNURF	11171	promoter
chr15	24953987	24954986	SNRPN	11164	promoter
chr19	56840727	56841726	PEG3	8826	promoter
chr20	58890421	58891420	GNAS	4392	promoter
chr1	17011758	17012757	ENSG00000288636	NA	promoter
chr1	21546404	21547403	ENSG00000289715	NA	promoter
chr1	23094377	23095376	ENSG00000293565	NA	promoter
chr1	30576826	30577825	ENSG00000289710	NA	promoter
chr1	31919629	31920628	ENSG00000288678	NA	promoter
chr1	41628817	41629816	ENSG00000284895	NA	promoter
chr1	53440019	53441018	ENSG00000293253	NA	promoter
chr1	89578592	89579591	ENSG00000288629	NA	promoter
chr1	147610590	147611589	ENSG00000288626	NA	promoter
chr1	155637605	155638604	ENSG00000287839	NA	promoter
chr1	174022299	174023298	ENSG00000293562	NA	promoter
chr1	179881316	179882315	ENSG00000293564	NA	promoter
chr1	203801094	203802093	ENSG00000288644	NA	promoter
chr2	111120153	111121152	ENSG00000293584	NA	promoter
chr2	202376112	202377111	ENSG00000289490	NA	promoter
chr2	236507477	236508476	IQCA1	NA	promoter
chr3	10248042	10249041	ENSG00000289763	NA	promoter
chr3	40311086	40312085	ENSG00000291315	NA	promoter
chr3	88058217	88059216	ENSG00000288654	NA	promoter
chr3	101685827	101686826	ENSG00000293268	NA	promoter
chr3	195909562	195910561	ENSG00000289747	NA	promoter
chr4	6070163	6071162	ENSG00000284684	NA	promoter
chr4	41143100	41144099	ENSG00000289761	NA	promoter
chr5	21484012	21485011	ENSG00000233974	NA	promoter
chr5	34189156	34190155	ENSG00000215156	NA	promoter
chr5	69631080	69632079	ENSG00000250138	NA	promoter
chr5	69903086	69904085	ENSG00000251158	NA	promoter
chr5	70486719	70487718	ENSG00000293691	NA	promoter
chr5	70507196	70508195	ENSG00000293689	NA	promoter
chr5	99525362	99526361	ENSG00000206356	NA	promoter
chr5	100387975	100388974	ENSG00000273957	NA	promoter
chr5	140563828	140564827	ENSG00000293600	NA	promoter
chr5	176083963	176084962	ENSG00000289731	NA	promoter
chr5	179521483	179522482	ENSG00000251545	NA	promoter
chr6	11093194	11094193	ENSG00000293642	NA	promoter
chr6	16328432	16329431	ENSG00000288708	NA	promoter
chr6	30933523	30934522	ENSG00000310558	NA	promoter
chr6	31621774	31622773	ENSG00000291302	NA	promoter
chr6	31622874	31623873	ENSG00000289282	NA	promoter
chr6	53041386	53042385	ENSG00000288614	NA	promoter
chr6	53064602	53065601	ENSG00000288646	NA	promoter
chr6	63571480	63572479	ENSG00000285976	NA	promoter
chr6	68634890	68635889	ENSG00000288712	NA	promoter
chr6	133952304	133953303	ENSG00000288529	NA	promoter
chr7	38273637	38274636	TARP	NA	promoter
chr7	100478171	100479170	ENSG00000289760	NA	promoter
chr7	105039848	105040847	ENSG00000289360	NA	promoter
chr7	105039858	105040857	ENSG00000288914	NA	promoter
chr7	112449487	112450486	ENSG00000288634	NA	promoter
chr7	150404676	150405675	ENSG00000284691	NA	promoter
chr7	151060928	151061927	ENSG00000288608	NA	promoter
chr8	32646202	32647201	ENSG00000286131	NA	promoter
chr8	102863861	102864860	ENSG00000289653	NA	promoter
chr8	109538726	109539725	ENSG00000289767	NA	promoter
chr9	34666046	34667045	ENSG00000187186	NA	promoter
chr9	87955214	87956213	ENSG00000283205	NA	promoter
chr9	130712626	130713625	ENSG00000288570	NA	promoter
chr9	131429129	131430128	ENSG00000291303	NA	promoter
chr9	131431759	131432758	ENSG00000288841	NA	promoter
chr9	135613183	135614182	ENSG00000236543	NA	promoter
chr9	137216494	137217493	ENSG00000284976	NA	promoter
chr10	66925308	66926307	ENSG00000289325	NA	promoter
chr11	804420	805419	ENSG00000293685	NA	promoter
chr11	2149604	2150603	ENSG00000284779	NA	promoter
chr11	64240095	64241094	ENSG00000286264	NA	promoter
chr12	13103485	13104484	ENSG00000289766	NA	promoter
chr12	13980896	13981895	ENSG00000293563	NA	promoter
chr12	31748391	31749390	ENSG00000300510	NA	promoter
chr12	53240900	53241899	ENSG00000283536	NA	promoter
chr12	57520481	57521480	ENSG00000285133	NA	promoter
chr12	111841237	111842236	ENSG00000292259	NA	promoter
chr12	113221095	113222094	IQCD	NA	promoter
chr12	120533697	120534696	ENSG00000288623	NA	promoter
chr12	122226565	122227564	ENSG00000284934	NA	promoter
chr13	63745741	63746740	ENSG00000237378	NA	promoter
chr13	63833054	63834053	ENSG00000285566	NA	promoter
chr13	77326989	77327988	ENSG00000288716	NA	promoter
chr14	61320954	61321953	ENSG00000310561	NA	promoter
chr14	92627967	92628966	ENSG00000293569	NA	promoter
chr14	103333237	103334236	ENSG00000291313	NA	promoter
chr15	50686718	50687717	ENSG00000288645	NA	promoter
chr15	52044846	52045845	ENSG00000289025	NA	promoter
chr15	81001142	81002141	ENSG00000288625	NA	promoter
chr16	3003132	3004131	ENSG00000289281	NA	promoter
chr16	11527248	11528247	ENSG00000188897	NA	promoter
chr16	30052151	30053150	ENSG00000285043	NA	promoter
chr16	30610352	30611351	ENSG00000289491	NA	promoter
chr16	89418293	89419292	ENSG00000288715	NA	promoter
chr17	6640317	6641316	ENSG00000282936	NA	promoter
chr17	76569649	76570648	ENSG00000284526	NA	promoter
chr17	80544075	80545074	ENSG00000289764	NA	promoter
chr18	21111140	21112139	ENSG00000293575	NA	promoter
chr19	20357163	20358162	ENSG00000293570	NA	promoter
chr19	39831957	39832956	ENSG00000291312	NA	promoter
chr19	52690497	52691496	ENSG00000269825	NA	promoter
chr20	10434223	10435222	ENSG00000285508	NA	promoter
chr20	10434223	10435222	ENSG00000285723	NA	promoter
chr20	32190361	32191360	ENSG00000293164	NA	promoter
chr21	34072576	34073575	ENSG00000293606	NA	promoter
chr21	43938919	43939918	ENSG00000288593	NA	promoter
chr21	46325288	46326287	ENSG00000286224	NA	promoter
chr22	39503231	39504230	MIURF	NA	promoter
chrX	10576956	10577955	ENSG00000291314	NA	promoter
chrX	23782278	23783277	ENSG00000288706	NA	promoter
chrX	40833445	40834444	ENSG00000300293	NA	promoter
chrX	45729995	45730994	ENSG00000310562	NA	promoter
chrX	63754665	63755664	ENSG00000288661	NA	promoter
chrX	120878925	120879924	ENSG00000278646	NA	promoter
chrX	135252012	135253011	ENSG00000293661	NA	promoter
chrX	135306259	135307258	ENSG00000293662	NA	promoter
chrX	135392208	135393207	ENSG00000293663	NA	promoter
chrX	149415507	149416506	ENSG00000287585	NA	promoter
GL000009.2	58377	59376	ENSG00000278704	NA	promoter
GL000194.1	115019	116018	ENSG00000277400	NA	promoter
GL000195.1	49165	50164	ENSG00000276256	NA	promoter
GL000213.1	139656	140655	ENSG00000277630	NA	promoter
GL000218.1	54894	55893	ENSG00000278384	NA	promoter
GL000219.1	83312	84311	ENSG00000273748	NA	promoter
KI270711.1	29627	30626	ENSG00000271254	NA	promoter
KI270713.1	32529	33528	ENSG00000277475	NA	promoter
KI270713.1	34407	35406	ENSG00000268674	NA	promoter
KI270721.1	1585	2584	ENSG00000276345	NA	promoter
KI270726.1	25241	26240	ENSG00000277856	NA	promoter
KI270726.1	40444	41443	ENSG00000275063	NA	promoter
KI270727.1	167568	168567	ENSG00000276760	NA	promoter
KI270727.1	371322	372321	ENSG00000275249	NA	promoter
KI270727.1	385278	386277	ENSG00000274792	NA	promoter
KI270728.1	16234	17233	ENSG00000274175	NA	promoter
KI270728.1	936468	937467	ENSG00000275869	NA	promoter
KI270728.1	1147869	1148868	ENSG00000273554	NA	promoter
KI270728.1	1269984	1270983	ENSG00000277836	NA	promoter
KI270731.1	13002	14001	ENSG00000278633	NA	promoter
KI270734.1	71411	72410	ENSG00000276017	NA	promoter
KI270734.1	130494	131493	ENSG00000278817	NA	promoter
KI270734.1	161853	162852	ENSG00000277196	NA	promoter