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#!/usr/bin/python3
"""
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__()
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