3/6/23 DL 

Measures enrichment/depletion of GWAS SNPS in TGIF boundaries
Run in order:
> cd snps
> python get_snps_by_parent_term.py
> cd ../
> ./map_snps_to_bins.sh
> ./get_snp_and_gene_list.sh
> ./get_enrichment.sh

snps/
	list of GWAS SNPs (see snps/README for more details)

bed/
	bed files with coordinates of each 10kb bin used in HiC data

map_snps_to_bins.py
map_snps_to_bins.sh
	script & wrapper to count the number of SNPs found in each 
	10kb bin

get_snp_and_gene_list.py
get_snp_and_gene_list.sh
	script to get the name of the SNP and its associated genes

map_snps_to_bins/
	output of map_snps_to_bins.sh and get_snp_and_gene_list.sh

get_enrichment.py
get_enrichment_intersection.py
get_enrichment_first2.py
get_enrichment_last2.py
get_enrichment_unique_bg.py
get_enrichment_unique.py
	script to test the enrichment of SNPs in TGIF boundaries 
	with different foreground(f) and background(b), in order:
	1. (f) union of boundaries across all timepoints (b) all genomic regions
	2. (f) intersection of boundaries (b) all genomic regions
	3. (f) intersection of boundaries in first 2 timeoints (b) all genomic regions
	4. (f) intersection of boundaries in last 2 timepoints (b) all genomic regions
	5. (f) boundaries unique to each timepoint (b) union of boundaries
	6. (f) boundaries unique to each timepoint (b) all genomic regions

enrichment/
	output of get_enrichment*.py scripts for each parent EFO term;
	each ouput file has the same suffix in the name as the script
	that generated it

get_enrichment.sh
	wrapper script to loop through each parent EFO term and any of 
	the get_enrichment*.py scripts
