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88 lines
2.9 KiB
Python
Executable File
88 lines
2.9 KiB
Python
Executable File
#!/usr/bin/env python
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"""
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Build a UCSC genome browser custom track file
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"""
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import sys, os
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assert sys.version_info[:2] >= ( 2, 4 )
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def stop_err( msg ):
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sys.stderr.write( msg )
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sys.exit()
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args = sys.argv[1:]
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out_fname = args.pop(0)
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out = open( out_fname, "w" )
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num_tracks = 0
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skipped_lines = 0
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first_invalid_line = 0
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while args:
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# Suck in one dataset worth of arguments
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in_fname = args.pop(0)
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type = args.pop(0)
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colspec = args.pop(0)
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name = args.pop(0)
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description = args.pop(0)
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color = args.pop(0).replace( '-', ',' )
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visibility = args.pop(0)
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# Do the work
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if type == "wig":
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print >> out, '''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s''' \
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% ( name, description, color, visibility )
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for i, line in enumerate( file( in_fname ) ):
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print >> out, line,
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print >> out
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elif type == "bed":
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print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
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% ( name, description, color, visibility )
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for i, line in enumerate( file( in_fname ) ):
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print >> out, line,
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print >> out
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else:
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# Assume type is interval (don't pass this script anything else!)
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try:
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c, s, e, st = [ int( x ) - 1 for x in colspec.split( "," ) ]
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except:
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try:
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c, s, e = [ int( x ) - 1 for x in colspec.split( "," )[:3] ]
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st = -1 #strand column is absent
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except:
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stop_err( "Columns in interval file invalid for UCSC custom track." )
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print >> out, '''track name="%s" description="%s" color=%s visibility=%s''' \
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% ( name, description, color, visibility )
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i = 0
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for i, line in enumerate( file( in_fname ) ):
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line = line.rstrip( '\r\n' )
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if line and not line.startswith( '#' ):
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fields = line.split( "\t" )
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if st > 0:
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#strand column is present
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try:
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print >> out, "%s\t%s\t%s\t%d\t0\t%s" % ( fields[c], fields[s], fields[e], i, fields[st] )
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except:
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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else:
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try:
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print >> out, "%s\t%s\t%s" % ( fields[c], fields[s], fields[e] )
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except:
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skipped_lines += 1
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if not first_invalid_line:
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first_invalid_line = i+1
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print >> out
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num_tracks += 1
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out.close()
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print "Generated a custom track containing %d subtracks." % num_tracks
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if skipped_lines:
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print "Skipped %d invalid lines starting at #%d" % ( skipped_lines, first_invalid_line )
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