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#!/usr/bin/python3
"""
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 = {}
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__()
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