galaxy/tools/maf/maf_limit_size.py

#!/usr/bin/env python
# Dan Blankenberg
"""
Removes blocks that fall outside of specified size range.
"""
from __future__ import print_function

import sys

import bx.align.maf


def __main__():
    input_maf_filename = sys.argv[1].strip()
    output_filename1 = sys.argv[2].strip()
    min_size = int(sys.argv[3].strip())
    max_size = int(sys.argv[4].strip())
    if max_size < 1:
        max_size = sys.maxsize
    maf_writer = bx.align.maf.Writer(open(output_filename1, "w"))
    try:
        maf_reader = bx.align.maf.Reader(open(input_maf_filename))
    except Exception:
        print("Your MAF file appears to be malformed.", file=sys.stderr)
        sys.exit()

    blocks_kept = 0
    i = 0
    for i, m in enumerate(maf_reader):  # noqa: B007
        if min_size <= m.text_size <= max_size:
            maf_writer.write(m)
            blocks_kept += 1
    print("Kept %s of %s blocks (%.2f%%)." % (blocks_kept, i + 1, float(blocks_kept) / float(i + 1) * 100.0))


if __name__ == "__main__":
    __main__()