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arq5x/test.py

Created September 6, 2011 01:11
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test
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test.py
from pybedtools import BedTool
snps = BedTool('../test/data/snps.bed.gz')
genes = BedTool('../test/data/hg19.gff')
intergenic_snps = (snps - genes)
nearby = genes.closest(intergenic_snps,
d=True,
stream=True)
for gene in nearby:
if int(gene[-1]) < 5000:
print gene.name
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