#!/opt/conda/conda-bld/bx-python_1659371818601/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_pla/bin/python

"""
Reads a list of intervals and a maf. Produces a new maf containing the
portions of the original that overlapped the intervals

NOTE: See maf_extract_ranges_indexed.py which works better / faster for many
      use cases.

TODO: Combine with maf_extract_ranges, and possibly share some code with
      maf_extract_ranges_indexed.

usage: %prog interval_file refname|refindex [options] < maf_file
   -m, --mincols=10: Minimum length (columns) required for alignment to be output
   -p, --prefix=PREFIX: Prefix
"""

import sys

import bx.align.maf
from bx import intervals
from bx.cookbook import doc_optparse


def __main__():
    options, args = doc_optparse.parse(__doc__)

    try:
        range_filename = args[0]
        try:
            refindex = int(args[1])
            refname = None
        except ValueError:
            refindex = None
            refname = args[1]
        if options.mincols:
            mincols = int(options.mincols)
        else:
            mincols = 10
        if options.prefix:
            prefix = options.prefix
        else:
            prefix = ""
    except Exception:
        doc_optparse.exit()

    # Load Intervals

    intersecters = dict()
    for line in open(range_filename):
        fields = line.split()
        src = prefix + fields[0]
        if src not in intersecters:
            intersecters[src] = intervals.Intersecter()
        intersecters[src].add_interval(intervals.Interval(int(fields[1]), int(fields[2])))

    # Start MAF on stdout

    out = bx.align.maf.Writer(sys.stdout)

    # Iterate over input MAF

    for maf in bx.align.maf.Reader(sys.stdin):
        if refname:
            sourcenames = [cmp.src.split('.')[0] for cmp in maf.components]
            try:
                refindex = sourcenames.index(refname)
            except Exception:
                continue

        ref_component = maf.components[refindex]
        # Find overlap with reference component
        if ref_component.src not in intersecters:
            continue
        intersections = sorted(intersecters[ref_component.src].find(ref_component.start, ref_component.end))
        # Keep output maf ordered
        # Write each intersecting block
        for interval in intersections:
            start = max(interval.start, ref_component.start)
            end = min(interval.end, ref_component.end)
            sliced = maf.slice_by_component(refindex, start, end)
            good = True
            for c in sliced.components:
                if c.size < 1:
                    good = False
            if good and sliced.text_size > mincols:
                out.write(sliced)

    # Close output MAF

    out.close()


if __name__ == "__main__":
    __main__()
