root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/EGG-INFO/scripts/axt_extract_ranges.py

#!/usr/bin/python2.6

"""
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 psyco_full

from bx.cookbook import doc_optparse

import bx.align.axt
from bx import intervals
import sys


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:
                doc_optparse.exit()

        # Load Intervals

        intersecter = intervals.Intersecter()
        for line in file( 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 = intersecter.find( ref_component.start, ref_component.end )
                # Keep output axt ordered
                intersections.sort()
                # 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__()