#!/opt/mambaforge/envs/bioconda/conda-bld/bx-python_1733805827733/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

"""
Filter each block in a maf file. Can filter blocks for a minimum number of
components (rows), a minimum length in columns, or an arbitrary python
expression (which will be evaluated for each block with the variable 'm'
containing that block).

usage: %prog [options] < maf > maf
    --component_count=N: Minimum number of components (rows)
    --min_cols=N: Minimum number of columns
    -e, --expr=EXPR: Python expression that must evaulate to true
"""

import sys
from optparse import OptionParser

from bx.align import maf


def __main__():
    # Parse command line arguments

    parser = OptionParser()
    parser.add_option("--component_count", action="store", default=None, type="int", help="")
    parser.add_option("--min_cols", action="store", default=None, type="int", help="")
    parser.add_option("-e", "--expr", action="store", default=None)

    (options, args) = parser.parse_args()

    component_count = options.component_count
    min_cols = options.min_cols
    expr = options.expr

    # Compile expression for SPEED
    if expr:
        expr = compile(expr, "<expr arg>", "eval")

    maf_reader = maf.Reader(sys.stdin, parse_e_rows=True)
    maf_writer = maf.Writer(sys.stdout)

    for m in maf_reader:
        if component_count and len(m.components) != component_count:
            continue
        if min_cols and m.text_size < min_cols:
            continue
        if expr and not bool(eval(expr, {"m": m, "maf": m})):
            continue

        maf_writer.write(m)


if __name__ == "__main__":
    __main__()
