Commit f536f68d authored by Mikael Boden's avatar Mikael Boden
parents ffe94c34 d3115c8d
#!/usr/bin/env python3
import seqdata, sys
expects as input arguments:
[1] filepath to chip-seq peaks (.bed)
[2] filepath to reference genome annotation file (of gene locations in genome) (.bed)
--dist maximum distance to consider binding to be significant to a gene (default, 300bp)
if len(sys.argv) < 3:
print('Usage: getclosestgene <chip-peak-bed-file> <reference-genome-annotation-file> [--dist <promoter region bp, default 300bp>]')
print('[] represents optional parameters')
# parse the input arguments
chipbedfile = sys.argv[1]
refgenelocfile = sys.argv[2]
dist = 300
if len(sys.argv) > 3 and sys.argv[3] == '--dist':
dist = sys.argv[4]
# load the chip seq peak bed file
sites = seqdata.BedFile(chipbedfile, 'Peaks')
# load the reference genome annotation file
genes = seqdata.BedFile(refgenelocfile, 'Optional')
# find the closest gene to each binding site and write to a bed output file
f = open('tss_gene.bed', 'w')
for site in sites:
geneInfo = genes.closest(site) # finds the closest gene to the binding site, returns a tuple
# detailing the distance and the BED file entry
# ignore if a null entry or if the distance is greater than the specified promoter region (dist)
if geneInfo == None or int(geneInfo[0]) > int(dist):
# record target gene if the binding site is upstream of the gene (this relies on strand information
# from the annotation file)
gene = geneInfo[1]
if (gene.strand == '+' and gene.chromStart >= site.chromStart) or (gene.strand == '-' and gene.chromStart <= site.chromStart):
entry = (site.chrom + '\t' + str(site.chromStart) + '\t' + str(site.chromEnd) + '\t'
+ + '\t' + str(geneInfo[0]) + '\t' + gene.strand + '\n')
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