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99 lines
3.8 KiB
Python
Executable File
99 lines
3.8 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Find regions of first interval file that overlap regions in a second interval file.
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Interval files can either be BED or GFF format.
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usage: %prog interval_file_1 interval_file_2 out_file
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-1, --cols1=N,N,N,N: Columns for start, end, strand in first file
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-2, --cols2=N,N,N,N: Columns for start, end, strand in second file
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-m, --mincols=N: Require this much overlap (default 1bp)
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-p, --pieces: just print pieces of second set (after padding)
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-G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
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-H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
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"""
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "bx-python" )
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import sys, traceback, fileinput
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from warnings import warn
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from bx.intervals import *
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from bx.intervals.io import *
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from bx.intervals.operations.intersect import *
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from bx.cookbook import doc_optparse
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from galaxy.tools.util.galaxyops import *
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from galaxy.datatypes.util.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
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assert sys.version_info[:2] >= ( 2, 4 )
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def main():
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mincols = 1
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upstream_pad = 0
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downstream_pad = 0
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options, args = doc_optparse.parse( __doc__ )
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try:
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chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
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chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
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if options.mincols: mincols = int( options.mincols )
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pieces = bool( options.pieces )
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in1_gff_format = bool( options.gff1 )
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in2_gff_format = bool( options.gff2 )
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in_fname, in2_fname, out_fname = args
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except:
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doc_optparse.exception()
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# Set readers to handle either GFF or default format.
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if in1_gff_format:
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in1_reader_wrapper = GFFReaderWrapper
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else:
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in1_reader_wrapper = NiceReaderWrapper
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if in2_gff_format:
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in2_reader_wrapper = GFFReaderWrapper
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else:
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in2_reader_wrapper = NiceReaderWrapper
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g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
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chrom_col=chr_col_1,
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start_col=start_col_1,
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end_col=end_col_1,
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strand_col=strand_col_1,
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fix_strand=True )
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if in1_gff_format:
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# Intersect requires coordinates in BED format.
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g1.convert_to_bed_coord=True
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g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
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chrom_col=chr_col_2,
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start_col=start_col_2,
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end_col=end_col_2,
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strand_col=strand_col_2,
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fix_strand=True )
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if in2_gff_format:
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# Intersect requires coordinates in BED format.
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g2.convert_to_bed_coord=True
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out_file = open( out_fname, "w" )
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try:
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for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
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if isinstance( feature, GFFFeature ):
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# Convert back to GFF coordinates since reader converted automatically.
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convert_bed_coords_to_gff( feature )
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for interval in feature.intervals:
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out_file.write( "%s\n" % "\t".join( interval.fields ) )
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elif isinstance( feature, GenomicInterval ):
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out_file.write( "%s\n" % "\t".join( feature.fields ) )
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else:
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out_file.write( "%s\n" % feature )
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except ParseError, e:
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out_file.close()
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fail( "Invalid file format: %s" % str( e ) )
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out_file.close()
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if g1.skipped > 0:
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print skipped( g1, filedesc=" of 1st dataset" )
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if g2.skipped > 0:
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print skipped( g2, filedesc=" of 2nd dataset" )
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if __name__ == "__main__":
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main()
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