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#!/usr/bin/python3
"""
Reads a list of intervals (start, stop) and a maf. Produces a new maf
containing the blocks from the original that overlapped the intervals.
NOTE: See maf_extract_ranges_indexed.py which works better / faster for many
use cases.
NOTE: chromosome/src information in the MAF is ignored by this variant.
NOTE: if a single alignment in a block become empty during slicing, the block
is ignored.
usage: %prog interval_file refindex [options] < maf_file
-m, --mincols=10: Minimum length (columns) required for alignment to be output
"""
import sys
import bx.align.maf
from bx import intervals
from bx.cookbook import doc_optparse
def __main__():
# Parse Command Line
options, args = doc_optparse.parse(__doc__)
try:
range_filename = args[0]
refindex = int(args[1])
if options.mincols:
mincols = int(options.mincols)
else:
mincols = 10
except Exception:
doc_optparse.exit()
# Load Intervals
intersecter = intervals.Intersecter()
for line in open(range_filename):
fields = line.split()
intersecter.add_interval(intervals.Interval(int(fields[0]), int(fields[1])))
# Start MAF on stdout
out = bx.align.maf.Writer(sys.stdout)
# Iterate over input MAF
for maf in bx.align.maf.Reader(sys.stdin, parse_e_rows=True):
ref = maf.components[refindex]
# Find overlap with reference component
intersections = sorted(intersecter.find(ref.get_forward_strand_start(), ref.get_forward_strand_end()))
# Keep output maf ordered
# Write each intersecting block
for interval in intersections:
start = max(interval.start, ref.get_forward_strand_start())
end = min(interval.end, ref.get_forward_strand_end())
sliced = maf.slice_by_component(refindex, start, end)
good = True
for c in sliced.components:
if c.size < 1 and not c.empty:
good = False
if good and sliced.text_size > mincols:
out.write(sliced)
# Close output MAF
out.close()
if __name__ == "__main__":
__main__()
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