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#!/usr/bin/python3
"""
Read a set of ranges and a nib file, print portions of nib overlapping
those ranges to stdout
TODO: General sequence handling would be nice, as well as merging with
'nib_intervals_to_fasta.py'.
usage: %prog nib_dir < range_file
"""
import sys
import bx.seq.nib
from bx.cookbook import doc_optparse
def __main__():
options, args = doc_optparse.parse(__doc__)
try:
nib_dir = args[0]
except IndexError:
doc_optparse.exit()
nibs = {}
for line in sys.stdin:
fields = line.split()
chrom, start, end = fields[0], int(fields[1]), int(fields[2])
print(">", chrom, start, end)
if chrom in nibs:
nib = nibs[chrom]
else:
nibs[chrom] = nib = bx.seq.nib.NibFile(open(f"{nib_dir}/{chrom}.nib"))
print_wrapped(nib.get(start, end - start))
def print_wrapped(s):
l = len(s)
c = 0
while c < l:
b = min(c + 50, l)
print(s[c:b])
c = b
if __name__ == "__main__":
__main__()
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