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comparison gops_cluster.py @ 0:d5677eecbad4

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Imported from capsule None
author devteam
date Tue, 01 Apr 2014 10:51:55 -0400
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children 765ceb06c3e2
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-1:000000000000 0:d5677eecbad4
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 import sys, traceback, fileinput
13 from warnings import warn
14 from bx.intervals import *
15 from bx.intervals.io import *
16 from bx.intervals.operations.find_clusters import *
17 from bx.cookbook import doc_optparse
18 from galaxy.tools.util.galaxyops import *
19
20 assert sys.version_info[:2] >= ( 2, 4 )
21
22 def main():
23 distance = 0
24 minregions = 2
25 output = 1
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 if options.distance: distance = int( options.distance )
33 if options.overlap: distance = -1 * int( options.overlap )
34 if options.output: output = int( options.output )
35 if options.minregions: minregions = int( options.minregions )
36 in_fname, out_fname = args
37 except:
38 doc_optparse.exception()
39
40 g1 = NiceReaderWrapper( fileinput.FileInput( in_fname ),
41 chrom_col=chr_col_1,
42 start_col=start_col_1,
43 end_col=end_col_1,
44 strand_col=strand_col_1,
45 fix_strand=True )
46
47 # Get the cluster tree
48 try:
49 clusters, extra = find_clusters( g1, mincols=distance, minregions=minregions)
50 except ParseError, exc:
51 fail( "Invalid file format: %s" % str( exc ) )
52
53 f1 = open( in_fname, "r" )
54 out_file = open( out_fname, "w" )
55
56 # If "merge"
57 if output == 1:
58 fields = ["." for x in range(max(g1.chrom_col, g1.start_col, g1.end_col)+1)]
59 for chrom, tree in clusters.items():
60 for start, end, lines in tree.getregions():
61 fields[g1.chrom_col] = chrom
62 fields[g1.start_col] = str(start)
63 fields[g1.end_col] = str(end)
64 out_file.write( "%s\n" % "\t".join( fields ) )
65
66 # If "filtered" we preserve order of file and comments, etc.
67 if output == 2:
68 linenums = dict()
69 for chrom, tree in clusters.items():
70 for linenum in tree.getlines():
71 linenums[linenum] = 0
72 linenum = -1
73 f1.seek(0)
74 for line in f1.readlines():
75 linenum += 1
76 if linenum in linenums or linenum in extra:
77 out_file.write( "%s\n" % line.rstrip( "\n\r" ) )
78
79 # If "clustered" we output original intervals, but near each other (i.e. clustered)
80 if output == 3:
81 linenums = list()
82 f1.seek(0)
83 fileLines = f1.readlines()
84 for chrom, tree in clusters.items():
85 for linenum in tree.getlines():
86 out_file.write( "%s\n" % fileLines[linenum].rstrip( "\n\r" ) )
87
88 # If "minimum" we output the smallest interval in each cluster
89 if output == 4 or output == 5:
90 linenums = list()
91 f1.seek(0)
92 fileLines = f1.readlines()
93 for chrom, tree in clusters.items():
94 regions = tree.getregions()
95 for start, end, lines in tree.getregions():
96 outsize = -1
97 outinterval = None
98 for line in lines:
99 # three nested for loops?
100 # should only execute this code once per line
101 fileline = fileLines[line].rstrip("\n\r")
102 try:
103 cluster_interval = GenomicInterval( g1, fileline.split("\t"),
104 g1.chrom_col,
105 g1.start_col,
106 g1.end_col,
107 g1.strand_col,
108 g1.default_strand,
109 g1.fix_strand )
110 except Exception, exc:
111 print >> sys.stderr, str( exc )
112 f1.close()
113 sys.exit()
114 interval_size = cluster_interval.end - cluster_interval.start
115 if outsize == -1 or \
116 ( outsize > interval_size and output == 4 ) or \
117 ( outsize < interval_size and output == 5 ) :
118 outinterval = cluster_interval
119 outsize = interval_size
120 out_file.write( "%s\n" % outinterval )
121
122 f1.close()
123 out_file.close()
124
125 if g1.skipped > 0:
126 print skipped( g1, filedesc="" )
127
128 if __name__ == "__main__":
129 main()