#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1720643686971/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

"""
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__()
