--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/build_ucsc_custom_track.py	Mon Jul 28 11:55:41 2014 -0400
@@ -0,0 +1,99 @@
+#!/usr/bin/env python
+"""
+Build a UCSC genome browser custom track file
+"""
+
+import sys, os
+
+assert sys.version_info[:2] >= ( 2, 4 )
+
+def stop_err( msg ):
+    sys.stderr.write( msg )
+    sys.exit()
+
+FILE_TYPE_TO_TRACK_TYPE = { 'bed': None, 'bedstrict': None, 'bed6': None, 'bed12': None, 'bedgraph':'bedGraph', 'wig':'wiggle_0' }
+CHUNK_SIZE = 2**20 #1mb
+
+def get_track_line_is_interval( file_type, name, description, color, visibility  ):
+    if file_type in FILE_TYPE_TO_TRACK_TYPE:
+        track_type = FILE_TYPE_TO_TRACK_TYPE[ file_type ]
+        is_interval = False
+    else:
+        track_type = None
+        is_interval = True
+    track_line = 'track '
+    if track_type:
+        track_line += 'type=%s ' % ( track_type )
+    track_line += 'name="%s" description="%s" color=%s visibility=%s\n' % ( name, description, color, visibility )
+    return track_line, is_interval
+
+args = sys.argv[1:]
+
+out_fname = args.pop(0)
+out = open( out_fname, "w" )
+
+num_tracks = 0
+skipped_lines = 0
+first_invalid_line = 0
+while args:
+    # Suck in one dataset worth of arguments
+    in_fname = args.pop(0)
+    file_type = args.pop(0)
+    colspec = args.pop(0)
+    name = args.pop(0)
+    description = args.pop(0)
+    color = args.pop(0).replace( '-', ',' )
+    visibility = args.pop(0)
+    track_line, is_interval = get_track_line_is_interval( file_type, name, description, color, visibility  )
+    # Do the work
+    in_file = open( in_fname )
+    out.write( track_line )
+    if not is_interval:
+        while True:
+            chunk = in_file.read( CHUNK_SIZE )
+            if chunk:
+                out.write( chunk )
+            else:
+                break
+    else:
+        # Assume type is interval (don't pass this script anything else!)
+        try:
+            c, s, e, st = [ int( x ) - 1 for x in colspec.split( "," ) ]
+        except:
+            try:
+                c, s, e = [ int( x ) - 1 for x in colspec.split( "," )[:3] ]
+                st = -1    #strand column is absent
+            except:
+                stop_err( "Columns in interval file invalid for UCSC custom track." )
+        
+        i = 0
+        for i, line in enumerate( in_file ):
+            line = line.rstrip( '\r\n' )
+            if line and not line.startswith( '#' ):
+                fields = line.split( "\t" )
+                if st > 0:
+                    #strand column is present
+                    try:
+                        out.write( "%s\t%s\t%s\t%d\t0\t%s\n" % ( fields[c], fields[s], fields[e], i, fields[st] ) )
+                    except:
+                        skipped_lines += 1
+                        if not first_invalid_line:
+                            first_invalid_line = i+1
+                else:
+                    try:
+                       out.write( "%s\t%s\t%s\n" % ( fields[c], fields[s], fields[e] ) )
+                    except:
+                        skipped_lines += 1
+                        if not first_invalid_line:
+                            first_invalid_line = i+1
+    out.write( "\n" ) #separating newline
+    num_tracks += 1
+    
+out.close()
+
+print "Generated a custom track containing %d subtracks." % num_tracks
+if skipped_lines:
+    print "Skipped %d invalid lines starting at #%d" % ( skipped_lines, first_invalid_line )
+
+
+