The BEDTools suite of programs is widely used for genomic interval manipulation or "genome algebra". pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.

See full online documentation, including installation instructions, at http://daler.github.io/pybedtools/.

Here is an example to get the names of genes that are <5 kb away from intergenic SNPs:

from pybedtools import BedTool

snps = BedTool('snps.bed.gz')  # [1]
genes = BedTool('hg19.gff')    # [1]

intergenic_snps = snps.subtract(genes)                       # [2]
nearby = genes.closest(intergenic_snps, d=True, stream=True) # [2, 3]

for gene in nearby:             # [4]
    if int(gene[-1]) < 5000:    # [4]
        print gene.name         # [4]

Useful features shown here include:

• [1] support for all BEDTools-supported formats (here gzipped BED and GFF)
• [2] wrapping of all BEDTools programs and arguments (here, subtract and closest and passing the -d flag to closest);
• [3] streaming results (like Unix pipes, here specified by stream=True)
• [4] iterating over results while accessing feature data by index or by attribute access (here [-1] and .name).

In contrast, here is the same analysis using shell scripting. Note that this requires knowledge in Perl, bash, and awk. The run time is identical to the pybedtools version above:

snps=snps.bed.gz
genes=hg19.gff
intergenic_snps=/tmp/intergenic_snps

snp_fields=`zcat $snps | awk '(NR == 2){print NF; exit;}'`
gene_fields=9
distance_field=$(($gene_fields + $snp_fields + 1))

intersectBed -a $snps -b $genes -v > $intergenic_snps

closestBed -a $genes -b $intergenic_snps -d \
| awk '($'$distance_field' < 5000){print $9;}' \
| perl -ne 'm/[ID|Name|gene_id]=(.*?);/; print "$1\n"'

rm $intergenic_snps

See the Shell script comparison in the docs for more details on this comparison, or keep reading the full documentation at http://daler.github.io/pybedtools.