Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/gops_coverage.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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() |