Mercurial > repos > xuebing > sharplabtool
comparison tools/visualization/build_ucsc_custom_track.py @ 0:9071e359b9a3
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| author | xuebing |
|---|---|
| date | Fri, 09 Mar 2012 19:37:19 -0500 |
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| children |
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| -1:000000000000 | 0:9071e359b9a3 |
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| 1 #!/usr/bin/env python | |
| 2 """ | |
| 3 Build a UCSC genome browser custom track file | |
| 4 """ | |
| 5 | |
| 6 import sys, os | |
| 7 | |
| 8 assert sys.version_info[:2] >= ( 2, 4 ) | |
| 9 | |
| 10 def stop_err( msg ): | |
| 11 sys.stderr.write( msg ) | |
| 12 sys.exit() | |
| 13 | |
| 14 args = sys.argv[1:] | |
| 15 | |
| 16 out_fname = args.pop(0) | |
| 17 out = open( out_fname, "w" ) | |
| 18 | |
| 19 num_tracks = 0 | |
| 20 skipped_lines = 0 | |
| 21 first_invalid_line = 0 | |
| 22 while 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 | |
| 80 out.close() | |
| 81 | |
| 82 print "Generated a custom track containing %d subtracks." % num_tracks | |
| 83 if skipped_lines: | |
| 84 print "Skipped %d invalid lines starting at #%d" % ( skipped_lines, first_invalid_line ) | |
| 85 | |
| 86 | |
| 87 |