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#!/usr/bin/python3
"""
Read BED file and extend each record to the specified minimum length. If chromosome
size information is provided trim extended intervals.
usage: %prog amount [ chrom_file ] < bed_file
"""
import sys
from bx.intervals.io import GenomicIntervalReader
length = int(sys.argv[1])
chrom_len = None
if len(sys.argv) > 2:
chrom_len = {fields[0]: int(fields[1]) for fields in map(str.split, open(sys.argv[2]))}
for interval in GenomicIntervalReader(sys.stdin):
if interval.end - interval.start < length:
start = interval.start
end = interval.end
# Extend in positive direction on strand
if interval.strand == "+":
end = start + length
else:
start = end - length
# Trim
if start < 0:
start = 0
if chrom_len and end > chrom_len[interval.chrom]:
end = chrom_len[interval.chrom]
# Set new start and end
interval.start = start
interval.end = end
# Output possibly adjusted interval
print(interval)
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