comparison tools/new_operations/gops_coverage.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 Calculate coverage of one query on another, and append the coverage to
4 the last two columns as bases covered and percent coverage.
5
6 usage: %prog bed_file_1 bed_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 """
10 from galaxy import eggs
11 import pkg_resources
12 pkg_resources.require( "bx-python" )
13 import sys, traceback, fileinput
14 from warnings import warn
15 from bx.intervals import *
16 from bx.intervals.io import *
17 from bx.intervals.operations.coverage import *
18 from bx.cookbook import doc_optparse
19 from galaxy.tools.util.galaxyops import *
20
21 assert sys.version_info[:2] >= ( 2, 4 )
22
23 def main():
24 upstream_pad = 0
25 downstream_pad = 0
26
27 options, args = doc_optparse.parse( __doc__ )
28 try:
29 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
30 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 )
31 in_fname, in2_fname, out_fname = args
32 except:
33 doc_optparse.exception()
34
35 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
36 chrom_col=chr_col_1,
37 start_col=start_col_1,
38 end_col=end_col_1,
39 strand_col=strand_col_1,
40 fix_strand=True )
41 g2 = NiceReaderWrapper( fileinput.FileInput( in2_fname ),
42 chrom_col=chr_col_2,
43 start_col=start_col_2,
44 end_col=end_col_2,
45 strand_col=strand_col_2,
46 fix_strand=True )
47
48 out_file = open( out_fname, "w" )
49
50 try:
51 for line in coverage( [g1,g2] ):
52 if type( line ) is GenomicInterval:
53 out_file.write( "%s\n" % "\t".join( line.fields ) )
54 else:
55 out_file.write( "%s\n" % line )
56 except ParseError, exc:
57 out_file.close()
58 fail( "Invalid file format: %s" % str( exc ) )
59
60 out_file.close()
61
62 if g1.skipped > 0:
63 print skipped( g1, filedesc=" of 1st dataset" )
64 if g2.skipped > 0:
65 print skipped( g2, filedesc=" of 2nd dataset" )
66
67 if __name__ == "__main__":
68 main()