root/galaxy-central/tools/extract/phastOdds/get_scores_galaxy.py @ 3

リビジョン 2, 5.1 KB (コミッタ: hatakeyama, 15 年 前)

import galaxy-central
  • 属性 svn:executable の設定値 *
行番号 
1#!/usr/bin/env python
2
3"""
4usage: %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
8from __future__ import division
9
10import sys
11from galaxy import eggs
12from numpy import *
13from tables import *
14
15import pkg_resources; pkg_resources.require( "bx-python" )
16from bx.cookbook import doc_optparse
17
18from bx import intervals
19
20# ignore wanrnings about NumArray flavor
21from warnings import filterwarnings
22from tables.exceptions import FlavorWarning
23filterwarnings("ignore", category=FlavorWarning)
24
25assert sys.version_info[:2] >= ( 2, 4 )
26
27def stop_err( msg ):
28    sys.stderr.write(msg)
29    sys.exit()
30
31def 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
147if __name__ == "__main__": main()
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