Mercurial > repos > xuebing > sharplabtool

comparison tools/new_operations/gops_join.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 """
3 Join two sets of intervals using their overlap as the key.
4
5 usage: %prog bed_file_1 bed_file_2 out_file
6 -1, --cols1=N,N,N,N: Columns for start, end, strand in first file
7 -2, --cols2=N,N,N,N: Columns for start, end, strand in second file
8 -m, --mincols=N: Require this much overlap (default 1bp)
9 -f, --fill=N: none, right, left, both
10 """
11 from galaxy import eggs
12 import pkg_resources
13 pkg_resources.require( "bx-python" )
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.join import *
19 from bx.cookbook import doc_optparse
20 from galaxy.tools.util.galaxyops import *
21
22 assert sys.version_info[:2] >= ( 2, 4 )
23
24 def main():
25 mincols = 1
26 upstream_pad = 0
27 downstream_pad = 0
28 leftfill = False
29 rightfill = False
30
31 options, args = doc_optparse.parse( __doc__ )
32 try:
33 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
34 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
35 if options.mincols: mincols = int( options.mincols )
36 if options.fill:
37 if options.fill == "both":
38 rightfill = leftfill = True
39 else:
40 rightfill = options.fill == "right"
41 leftfill = options.fill == "left"
42 in_fname, in2_fname, out_fname = args
43 except:
44 doc_optparse.exception()
45
46 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
47 chrom_col=chr_col_1,
48 start_col=start_col_1,
49 end_col=end_col_1,
50 strand_col=strand_col_1,
51 fix_strand=True )
52 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
53 chrom_col=chr_col_2,
54 start_col=start_col_2,
55 end_col=end_col_2,
56 strand_col=strand_col_2,
57 fix_strand=True )
58
59 out_file = open( out_fname, "w" )
60
61 try:
62 for outfields in join(g1, g2, mincols=mincols, rightfill=rightfill, leftfill=leftfill):
63 if type( outfields ) is list:
64 out_file.write( "%s\n" % "\t".join( outfields ) )
65 else:
66 out_file.write( "%s\n" % outfields )
67 except ParseError, exc:
68 out_file.close()
69 fail( "Invalid file format: %s" % str( exc ) )
70 except MemoryError:
71 out_file.close()
72 fail( "Input datasets were too large to complete the join operation." )
73
74 out_file.close()
75
76 if g1.skipped > 0:
77 print skipped( g1, filedesc=" of 1st dataset" )
78 if g2.skipped > 0:
79 print skipped( g2, filedesc=" of 2nd dataset" )
80
81 if __name__ == "__main__":
82 main()