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#!/usr/bin/python3
"""
Reads a list of intervals and an axt. Produces a new axt containing the
portions of the original that overlapped the intervals
usage: %prog interval_file refindex [options] < axt_file
-m, --mincols=10: Minimum length (columns) required for alignment to be output
"""
import sys
import bx.align.axt
from bx import intervals
from bx.cookbook import doc_optparse
def __main__():
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 axt on stdout
out = bx.align.axt.Writer(sys.stdout)
# Iterate over input axt
for axt in bx.align.axt.Reader(sys.stdin):
ref_component = axt.components[refindex]
# Find overlap with reference component
intersections = sorted(intersecter.find(ref_component.start, ref_component.end))
# Keep output axt ordered
# Write each intersecting block
for interval in intersections:
start = max(interval.start, ref_component.start)
end = min(interval.end, ref_component.end)
sliced = axt.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 axt
out.close()
if __name__ == "__main__":
__main__()
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