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comparison gops_intersect.py @ 0:5b3c6135a982

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:53:10 -0400
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children 5f72be09cfd3
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-1:000000000000 0:5b3c6135a982
1 #!/usr/bin/env python
2 """
3 Find regions of first interval file that overlap regions in a second interval file.
4 Interval files can either be BED or GFF format.
5
6 usage: %prog interval_file_1 interval_file_2 out_file
7 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
8 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
9 -m, --mincols=N: Require this much overlap (default 1bp)
10 -p, --pieces: just print pieces of second set (after padding)
11 -G, --gff1: input 1 is GFF format, meaning start and end coordinates are 1-based, closed interval
12 -H, --gff2: input 2 is GFF format, meaning start and end coordinates are 1-based, closed interval
13 """
14 import sys, traceback, fileinput
15 from warnings import warn
16 from bx.intervals import *
17 from bx.intervals.io import *
18 from bx.intervals.operations.intersect import *
19 from bx.cookbook import doc_optparse
20 from galaxy.tools.util.galaxyops import *
21 from utils.gff_util import GFFFeature, GFFReaderWrapper, convert_bed_coords_to_gff
22
23 assert sys.version_info[:2] >= ( 2, 4 )
24
25 def main():
26 mincols = 1
27 upstream_pad = 0
28 downstream_pad = 0
29
30 options, args = doc_optparse.parse( __doc__ )
31 try:
32 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
33 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
34 if options.mincols: mincols = int( options.mincols )
35 pieces = bool( options.pieces )
36 in1_gff_format = bool( options.gff1 )
37 in2_gff_format = bool( options.gff2 )
38 in_fname, in2_fname, out_fname = args
39 except:
40 doc_optparse.exception()
41
42 # Set readers to handle either GFF or default format.
43 if in1_gff_format:
44 in1_reader_wrapper = GFFReaderWrapper
45 else:
46 in1_reader_wrapper = NiceReaderWrapper
47 if in2_gff_format:
48 in2_reader_wrapper = GFFReaderWrapper
49 else:
50 in2_reader_wrapper = NiceReaderWrapper
51
52 g1 = in1_reader_wrapper( fileinput.FileInput( in_fname ),
53 chrom_col=chr_col_1,
54 start_col=start_col_1,
55 end_col=end_col_1,
56 strand_col=strand_col_1,
57 fix_strand=True )
58 if in1_gff_format:
59 # Intersect requires coordinates in BED format.
60 g1.convert_to_bed_coord=True
61 g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
62 chrom_col=chr_col_2,
63 start_col=start_col_2,
64 end_col=end_col_2,
65 strand_col=strand_col_2,
66 fix_strand=True )
67 if in2_gff_format:
68 # Intersect requires coordinates in BED format.
69 g2.convert_to_bed_coord=True
70
71 out_file = open( out_fname, "w" )
72 try:
73 for feature in intersect( [g1,g2], pieces=pieces, mincols=mincols ):
74 if isinstance( feature, GFFFeature ):
75 # Convert back to GFF coordinates since reader converted automatically.
76 convert_bed_coords_to_gff( feature )
77 for interval in feature.intervals:
78 out_file.write( "%s\n" % "\t".join( interval.fields ) )
79 elif isinstance( feature, GenomicInterval ):
80 out_file.write( "%s\n" % "\t".join( feature.fields ) )
81 else:
82 out_file.write( "%s\n" % feature )
83 except ParseError, e:
84 out_file.close()
85 fail( "Invalid file format: %s" % str( e ) )
86
87 out_file.close()
88
89 if g1.skipped > 0:
90 print skipped( g1, filedesc=" of 1st dataset" )
91 if g2.skipped > 0:
92 print skipped( g2, filedesc=" of 2nd dataset" )
93
94 if __name__ == "__main__":
95 main()