Mercurial > repos > xuebing > sharplabtool

comparison tools/extract/phastOdds/get_scores_galaxy.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 """
4 usage: %prog data_file.h5 region_mapping.bed in_file out_file chrom_col start_col end_col [options]
5 -p, --perCol: standardize to lod per column
6 """
7
8 from __future__ import division
9
10 import sys
11 from galaxy import eggs
12 from numpy import *
13 from tables import *
14
15 import pkg_resources; pkg_resources.require( "bx-python" )
16 from bx.cookbook import doc_optparse
17
18 from bx import intervals
19
20 # ignore wanrnings about NumArray flavor
21 from warnings import filterwarnings
22 from tables.exceptions import FlavorWarning
23 filterwarnings("ignore", category=FlavorWarning)
24
25 assert sys.version_info[:2] >= ( 2, 4 )
26
27 def stop_err( msg ):
28 sys.stderr.write(msg)
29 sys.exit()
30
31 def main():
32 # Parse command line
33 options, args = doc_optparse.parse( __doc__ )
34 try:
35 h5_fname = args[0]
36 mapping_fname = args[1]
37 in_fname = args[2]
38 out_fname = args[3]
39 chrom_col, start_col, end_col = map( lambda x: int( x ) - 1, args[4:7] )
40 per_col = bool( options.perCol )
41 except Exception, e:
42 doc_optparse.exception()
43
44 if h5_fname == 'None.h5':
45 stop_err( 'Invalid genome build, this tool currently only works with data from build hg17. Click the pencil icon in your history item to correct the build if appropriate.' )
46
47 # Open the h5 file
48 h5 = openFile( h5_fname, mode = "r" )
49 # Load intervals and names for the subregions
50 intersecters = {}
51 for i, line in enumerate( file( mapping_fname ) ):
52 line = line.rstrip( '\r\n' )
53 if line and not line.startswith( '#' ):
54 chr, start, end, name = line.split()[0:4]
55 if not intersecters.has_key( chr ):
56 intersecters[ chr ] = intervals.Intersecter()
57 intersecters[ chr ].add_interval( intervals.Interval( int( start ), int( end ), name ) )
58
59 # Find the subregion containing each input interval
60 skipped_lines = 0
61 first_invalid_line = 0
62 invalid_line = ''
63 out_file = open( out_fname, "w" )
64 warnings = []
65 warning = ''
66 for i, line in enumerate( file( in_fname ) ):
67 line = line.rstrip( '\r\n' )
68 if line.startswith( '#' ):
69 if i == 0:
70 out_file.write( "%s\tscore\n" % line )
71 else:
72 out_file.write( "%s\n" % line )
73 fields = line.split( "\t" )
74 try:
75 chr = fields[ chrom_col ]
76 start = int( fields[ start_col ] )
77 end = int( fields[ end_col ] )
78 except:
79 warning = "Invalid value for chrom, start or end column."
80 warnings.append( warning )
81 skipped_lines += 1
82 if not invalid_line:
83 first_invalid_line = i + 1
84 invalid_line = line
85 continue
86 # Find matching interval
87 try:
88 matches = intersecters[ chr ].find( start, end )
89 except:
90 warning = "'%s' is not a valid chrom value for the region. " %chr
91 warnings.append( warning )
92 skipped_lines += 1
93 if not invalid_line:
94 first_invalid_line = i + 1
95 invalid_line = line
96 continue
97 if not len( matches ) == 1:
98 warning = "Interval must match exactly one target region. "
99 warnings.append( warning )
100 skipped_lines += 1
101 if not invalid_line:
102 first_invalid_line = i + 1
103 invalid_line = line
104 continue
105 region = matches[0]
106 if not ( start >= region.start and end <= region.end ):
107 warning = "Interval must fall entirely within region. "
108 warnings.append( warning )
109 skipped_lines += 1
110 if not invalid_line:
111 first_invalid_line = i + 1
112 invalid_line = line
113 continue
114 region_name = region.value
115 rel_start = start - region.start
116 rel_end = end - region.start
117 if not rel_start < rel_end:
118 warning = "Region %s is empty, relative start:%d, relative end:%d. " % ( region_name, rel_start, rel_end )
119 warnings.append( warning )
120 skipped_lines += 1
121 if not invalid_line:
122 first_invalid_line = i + 1
123 invalid_line = line
124 continue
125 s = h5.getNode( h5.root, "scores_" + region_name )
126 c = h5.getNode( h5.root, "counts_" + region_name )
127 score = s[rel_end-1]
128 count = c[rel_end-1]
129 if rel_start > 0:
130 score -= s[rel_start-1]
131 count -= c[rel_start-1]
132 if per_col:
133 score /= count
134 fields.append( str( score ) )
135 out_file.write( "%s\n" % "\t".join( fields ) )
136 # Close the file handle
137 h5.close()
138 out_file.close()
139
140 if warnings:
141 warn_msg = "PhastOdds scores are only available for ENCODE regions. %d warnings, 1st is: " % len( warnings )
142 warn_msg += warnings[0]
143 print warn_msg
144 if skipped_lines:
145 print 'Skipped %d invalid lines, 1st is #%d, "%s"' % ( skipped_lines, first_invalid_line, invalid_line )
146
147 if __name__ == "__main__": main()