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

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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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()