root/galaxy-central/tools/visualization/build_ucsc_custom_track.py

リビジョン 2, 2.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

  • 属性 svn:executable の設定値 *
行番号 
1#!/usr/bin/env python
2"""
3Build a UCSC genome browser custom track file
4"""
5
6import sys, os
7
8assert sys.version_info[:2] >= ( 2, 4 )
9
10def stop_err( msg ):
11    sys.stderr.write( msg )
12    sys.exit()
13
14args = sys.argv[1:]
15
16out_fname = args.pop(0)
17out = open( out_fname, "w" )
18
19num_tracks = 0
20skipped_lines = 0
21first_invalid_line = 0
22while args:
23    # Suck in one dataset worth of arguments
24    in_fname = args.pop(0)
25    type = args.pop(0)
26    colspec = args.pop(0)
27    name = args.pop(0)
28    description = args.pop(0)
29    color = args.pop(0).replace( '-', ',' )
30    visibility = args.pop(0)
31    # Do the work
32    if type == "wig":
33        print >> out, '''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s''' \
34                      % ( name, description, color, visibility )
35        for i, line in enumerate( file( in_fname ) ):
36            print >> out, line,
37        print >> out
38    elif type == "bed":
39        print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
40                      % ( name, description, color, visibility )
41        for i, line in enumerate( file( in_fname ) ):
42            print >> out, line,
43        print >> out
44    else:
45        # Assume type is interval (don't pass this script anything else!)
46        try:
47            c, s, e, st = [ int( x ) - 1 for x in colspec.split( "," ) ]
48        except:
49            try:
50                c, s, e = [ int( x ) - 1 for x in colspec.split( "," )[:3] ]
51                st = -1    #strand column is absent
52            except:
53                stop_err( "Columns in interval file invalid for UCSC custom track." )
54       
55        print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
56                      % ( name, description, color, visibility )
57        i = 0
58        for i, line in enumerate( file( in_fname ) ):
59            line = line.rstrip( '\r\n' )
60            if line and not line.startswith( '#' ):
61                fields = line.split( "\t" )
62                if st > 0:
63                    #strand column is present
64                    try:
65                        print >> out, "%s\t%s\t%s\t%d\t0\t%s" % ( fields[c], fields[s], fields[e], i, fields[st] )
66                    except:
67                        skipped_lines += 1
68                        if not first_invalid_line:
69                            first_invalid_line = i+1
70                else:
71                    try:
72                        print >> out, "%s\t%s\t%s" % ( fields[c], fields[s], fields[e] )
73                    except:
74                        skipped_lines += 1
75                        if not first_invalid_line:
76                            first_invalid_line = i+1
77        print >> out
78    num_tracks += 1
79   
80out.close()
81
82print "Generated a custom track containing %d subtracks." % num_tracks
83if skipped_lines:
84    print "Skipped %d invalid lines starting at #%d" % ( skipped_lines, first_invalid_line )
85
86
87
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