Mercurial > repos > xuebing > sharplabtool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:9071e359b9a3
1 #!/usr/bin/env python
2 """
3 Cluster regions of intervals.
4
5 usage: %prog in_file out_file
6 -1, --cols1=N,N,N,N: Columns for start, end, strand in file
7 -d, --distance=N: Maximum distance between clustered intervals
8 -v, --overlap=N: Minimum overlap require (negative distance)
9 -m, --minregions=N: Minimum regions per cluster
10 -o, --output=N: 1)merged 2)filtered 3)clustered 4) minimum 5) maximum
11 """
12 from galaxy import eggs
13 import pkg_resources
14 pkg_resources.require( "bx-python" )
15 import sys, traceback, fileinput
16 from warnings import warn
17 from bx.intervals import *
18 from bx.intervals.io import *
19 from bx.intervals.operations.find_clusters import *
20 from bx.cookbook import doc_optparse
21 from galaxy.tools.util.galaxyops import *
22
23 assert sys.version_info[:2] >= ( 2, 4 )
24
25 def main():
26 distance = 0
27 minregions = 2
28 output = 1
29 upstream_pad = 0
30 downstream_pad = 0
31
32 options, args = doc_optparse.parse( __doc__ )
33 try:
34 chr_col_1, start_col_1, end_col_1, strand_col_1 = parse_cols_arg( options.cols1 )
35 if options.distance: distance = int( options.distance )
36 if options.overlap: distance = -1 * int( options.overlap )
37 if options.output: output = int( options.output )
38 if options.minregions: minregions = int( options.minregions )
39 in_fname, out_fname = args
40 except:
41 doc_optparse.exception()
42
43 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
44 chrom_col=chr_col_1,
45 start_col=start_col_1,
46 end_col=end_col_1,
47 strand_col=strand_col_1,
48 fix_strand=True )
49
50 # Get the cluster tree
51 try:
52 clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
53 except ParseError, exc:
54 fail( "Invalid file format: %s" % str( exc ) )
55
56 f1 = open( in_fname, "r" )
57 out_file = open( out_fname, "w" )
58
59 # If "merge"
60 if output == 1:
61 fields = ["." for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
62 for chrom, tree in clusters.items():
63 for start, end, lines in tree.getregions():
64 fields[g1.chrom_col] = chrom
65 fields[g1.start_col] = str(start)
66 fields[g1.end_col] = str(end)
67 out_file.write( "%s\n" % "\t".join( fields ) )
68
69 # If "filtered" we preserve order of file and comments, etc.
70 if output == 2:
71 linenums = dict()
72 for chrom, tree in clusters.items():
73 for linenum in tree.getlines():
74 linenums[linenum] = 0
75 linenum = -1
76 f1.seek(0)
77 for line in f1.readlines():
78 linenum += 1
79 if linenum in linenums or linenum in extra:
80 out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
81
82 # If "clustered" we output original intervals, but near each other (i.e. clustered)
83 if output == 3:
84 linenums = list()
85 f1.seek(0)
86 fileLines = f1.readlines()
87 for chrom, tree in clusters.items():
88 for linenum in tree.getlines():
89 out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
90
91 # If "minimum" we output the smallest interval in each cluster
92 if output == 4 or output == 5:
93 linenums = list()
94 f1.seek(0)
95 fileLines = f1.readlines()
96 for chrom, tree in clusters.items():
97 regions = tree.getregions()
98 for start, end, lines in tree.getregions():
99 outsize = -1
100 outinterval = None
101 for line in lines:
102 # three nested for loops?
103 # should only execute this code once per line
104 fileline = fileLines[line].rstrip("\n\r")
105 try:
106 cluster_interval = GenomicInterval( g1, fileline.split("\t"),
107 g1.chrom_col,
108 g1.start_col,
109 g1.end_col,
110 g1.strand_col,
111 g1.default_strand,
112 g1.fix_strand )
113 except Exception, exc:
114 print >> sys.stderr, str( exc )
115 f1.close()
116 sys.exit()
117 interval_size = cluster_interval.end - cluster_interval.start
118 if outsize == -1 or \
119 ( outsize > interval_size and output == 4 ) or \
120 ( outsize < interval_size and output == 5 ) :
121 outinterval = cluster_interval
122 outsize = interval_size
123 out_file.write( "%s\n" % outinterval )
124
125 f1.close()
126 out_file.close()
127
128 if g1.skipped > 0:
129 print skipped( g1, filedesc="" )
130
131 if __name__ == "__main__":
132 main()