create regulatory domains

This is an example of code enables to create gene regulatory domains from several files.

Both files must be in .bed format documentation here: http://genome.ucsc.edu/FAQ/FAQformat#format1

Columns for tss_file should be : chr \t start \t end

association_rule could be : "one_closet" , "two_closet" and "basal_plus_extention"

[1]:

%load_ext autoreload
%autoreload 2

[2]:

import greatpy as great

For hg38

[3]:

regdom_hg38 = great.tl.create_regdom(
    tss_file = "../data/human/hg38/tss_from_great.bed",
    chr_sizes_file = "../data/human/hg38/chr_size.bed",
    association_rule = "basal_plus_extention",
    out_path = None
    )
regdom_hg38

[3]:

	chr	chr_start	chr_end	name	tss	strand
ENSG00000186092	chr1	0	450697	OR4F5	65418	+
ENSG00000284733	chr1	66418	685673	OR4F29	451697	-
ENSG00000284662	chr1	456697	920737	OR4F16	686673	-
ENSG00000187634	chr1	691673	958290	SAMD11	925737	+
ENSG00000188976	chr1	926737	964290	NOC2L	959290	-
...	...	...	...	...	...	...
ENSG00000183795	chrY	24052969	24812479	BPY2B	24618003	+
ENSG00000187191	chrY	24619003	24828916	DAZ3	24813479	-
ENSG00000205916	chrY	24818479	25051104	DAZ4	24833916	+
ENSG00000185894	chrY	24834916	25617161	BPY2C	25052104	-
ENSG00000172288	chrY	25057104	26622161	CDY1	25622161	+

18777 rows × 6 columns

For hg19

[4]:

regdom_hg19 = great.tl.create_regdom(
    tss_file = "../data/human/hg19/tss.bed",
    chr_sizes_file = "../data/human/hg19/chr_size.bed",
    association_rule = "basal_plus_extention",
    out_path = None
    )
regdom_hg19

[4]:

	chr	chr_start	chr_end	name	tss	strand
ENSG00000186092	chr1	0	362639	OR4F5	69090	+
ENSG00000235249	chr1	70090	621053	OR4F29	367639	+
ENSG00000185097	chr1	368639	856117	OR4F16	622053	-
ENSG00000187634	chr1	627053	893670	SAMD11	861117	+
ENSG00000188976	chr1	862117	899670	NOC2L	894670	-
...	...	...	...	...	...	...
ENSG00000183795	chrY	26199116	26958626	BPY2B	26764150	+
ENSG00000187191	chrY	26765150	26975080	DAZ3	26959626	-
ENSG00000205916	chrY	26964626	27197251	DAZ4	26980080	+
ENSG00000185894	chrY	26981080	27763308	BPY2C	27198251	-
ENSG00000172288	chrY	27203251	28768308	CDY1	27768308	+

18549 rows × 6 columns