|
0
|
1 #!/usr/bin/env python
|
|
|
2 """
|
|
|
3 Find regions of first interval file that do not overlap regions in a second
|
|
|
4 interval file. 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.subtract 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 # Subtract requires coordinates in BED format.
|
|
|
60 g1.convert_to_bed_coord=True
|
|
|
61
|
|
|
62 g2 = in2_reader_wrapper( fileinput.FileInput( in2_fname ),
|
|
|
63 chrom_col=chr_col_2,
|
|
|
64 start_col=start_col_2,
|
|
|
65 end_col=end_col_2,
|
|
|
66 strand_col=strand_col_2,
|
|
|
67 fix_strand=True )
|
|
|
68 if in2_gff_format:
|
|
|
69 # Subtract requires coordinates in BED format.
|
|
|
70 g2.convert_to_bed_coord=True
|
|
|
71
|
|
|
72 out_file = open( out_fname, "w" )
|
|
|
73 try:
|
|
|
74 for feature in subtract( [g1,g2], pieces=pieces, mincols=mincols ):
|
|
|
75 if isinstance( feature, GFFFeature ):
|
|
|
76 # Convert back to GFF coordinates since reader converted automatically.
|
|
|
77 convert_bed_coords_to_gff( feature )
|
|
|
78 for interval in feature.intervals:
|
|
|
79 out_file.write( "%s\n" % "\t".join( interval.fields ) )
|
|
|
80 elif isinstance( feature, GenomicInterval ):
|
|
|
81 out_file.write( "%s\n" % "\t".join( feature.fields ) )
|
|
|
82 else:
|
|
|
83 out_file.write( "%s\n" % feature )
|
|
|
84 except ParseError, exc:
|
|
|
85 out_file.close()
|
|
|
86 fail( "Invalid file format: %s" % str( exc ) )
|
|
|
87
|
|
|
88 out_file.close()
|
|
|
89
|
|
|
90 if g1.skipped > 0:
|
|
|
91 print skipped( g1, filedesc=" of 2nd dataset" )
|
|
|
92 if g2.skipped > 0:
|
|
|
93 print skipped( g2, filedesc=" of 1st dataset" )
|
|
|
94
|
|
|
95 if __name__ == "__main__":
|
|
|
96 main()
|
