Mercurial > repos > xuebing > sharplabtool

comparison tools/new_operations/gops_complement.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 Complement regions.
4
5 usage: %prog in_file out_file
6 -1, --cols1=N,N,N,N: Columns for chrom, start, end, strand in file
7 -l, --lengths=N: Filename of .len file for species (chromosome lengths)
8 -a, --all: Complement all chromosomes (Genome-wide complement)
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.complement import complement
18 from bx.intervals.operations.subtract import subtract
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 allchroms = False
26 upstream_pad = 0
27 downstream_pad = 0
28
29 options, args = doc_optparse.parse( __doc__ )
30 try:
31 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
32 lengths = options.lengths
33 if options.all: allchroms = True
34 in_fname, out_fname = args
35 except:
36 doc_optparse.exception()
37
38 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
39 chrom_col=chr_col_1,
40 start_col=start_col_1,
41 end_col=end_col_1,
42 strand_col=strand_col_1,
43 fix_strand=True )
44
45 lens = dict()
46 chroms = list()
47 # dbfile is used to determine the length of each chromosome. The lengths
48 # are added to the lens dict and passed copmlement operation code in bx.
49 dbfile = fileinput.FileInput( lengths )
50
51 if dbfile:
52 if not allchroms:
53 try:
54 for line in dbfile:
55 fields = line.split("\t")
56 lens[fields[0]] = int(fields[1])
57 except:
58 # assume LEN doesn't exist or is corrupt somehow
59 pass
60 elif allchroms:
61 try:
62 for line in dbfile:
63 fields = line.split("\t")
64 end = int(fields[1])
65 chroms.append("\t".join([fields[0],"0",str(end)]))
66 except:
67 pass
68
69 # Safety...if the dbfile didn't exist and we're on allchroms, then
70 # default to generic complement
71 if allchroms and len(chroms) == 0:
72 allchroms = False
73
74 if allchroms:
75 chromReader = GenomicIntervalReader(chroms)
76 generator = subtract([chromReader, g1])
77 else:
78 generator = complement(g1, lens)
79
80 out_file = open( out_fname, "w" )
81
82 try:
83 for interval in generator:
84 if type( interval ) is GenomicInterval:
85 out_file.write( "%s\n" % "\t".join( interval ) )
86 else:
87 out_file.write( "%s\n" % interval )
88 except ParseError, exc:
89 out_file.close()
90 fail( "Invalid file format: %s" % str( exc ) )
91
92 out_file.close()
93
94 if g1.skipped > 0:
95 print skipped( g1, filedesc="" )
96
97 if __name__ == "__main__":
98 main()