Mercurial > repos > xuebing > sharplabtool
comparison tools/new_operations/gops_concat.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 Concatenate two bed files. The concatenated files are returned in the | |
4 same format as the first. If --sameformat is specified, then all | |
5 columns will be treated as the same, and all fields will be saved, | |
6 although the output will be trimmed to match the primary input. In | |
7 addition, if --sameformat is specified, missing fields will be padded | |
8 with a period(.). | |
9 | |
10 usage: %prog in_file_1 in_file_2 out_file | |
11 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in first file | |
12 -2, --cols2=N,N,N,N: Columns for chrom, start, end, strand in second file | |
13 -s, --sameformat: All files are precisely the same format. | |
14 """ | |
15 from galaxy import eggs | |
16 import pkg_resources | |
17 pkg_resources.require( "bx-python" ) | |
18 import sys, traceback, fileinput | |
19 from warnings import warn | |
20 from bx.intervals import * | |
21 from bx.intervals.io import * | |
22 from bx.intervals.operations.concat import * | |
23 from bx.cookbook import doc_optparse | |
24 from galaxy.tools.util.galaxyops import * | |
25 | |
26 assert sys.version_info[:2] >= ( 2, 4 ) | |
27 | |
28 def main(): | |
29 sameformat=False | |
30 upstream_pad = 0 | |
31 downstream_pad = 0 | |
32 | |
33 options, args = doc_optparse.parse( __doc__ ) | |
34 try: | |
35 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 ) | |
36 chr_col_2, start_col_2, end_col_2, strand_col_2 = parse_cols_arg( options.cols2 ) | |
37 if options.sameformat: sameformat = True | |
38 in_file_1, in_file_2, out_fname = args | |
39 except: | |
40 doc_optparse.exception() | |
41 | |
42 g1 = NiceReaderWrapper( fileinput.FileInput( in_file_1 ), | |
43 chrom_col=chr_col_1, | |
44 start_col=start_col_1, | |
45 end_col=end_col_1, | |
46 fix_strand=True ) | |
47 | |
48 g2 = NiceReaderWrapper( fileinput.FileInput( in_file_2 ), | |
49 chrom_col=chr_col_2, | |
50 start_col=start_col_2, | |
51 end_col=end_col_2, | |
52 strand_col=strand_col_2, | |
53 fix_strand=True ) | |
54 | |
55 if strand_col_1 >= 0: | |
56 g1.strand_col = strand_col_1 | |
57 | |
58 out_file = open( out_fname, "w" ) | |
59 | |
60 try: | |
61 for line in concat( [g1, g2], sameformat=sameformat ): | |
62 if type( line ) is GenomicInterval: | |
63 out_file.write( "%s\n" % "\t".join( line.fields ) ) | |
64 else: | |
65 out_file.write( "%s\n" % line ) | |
66 except ParseError, exc: | |
67 out_file.close() | |
68 fail( "Invalid file format: %s" % str( exc ) ) | |
69 | |
70 out_file.close() | |
71 | |
72 if g1.skipped > 0: | |
73 print skipped( g1, filedesc=" of 1st dataset" ) | |
74 if g2.skipped > 0: | |
75 print skipped( g2, filedesc=" of 2nd dataset" ) | |
76 | |
77 if __name__ == "__main__": | |
78 main() |