Applied patch provided by Brad Chapman in the liftOver tool to support BED files that contain track or browser lines. Resolves bitbucket issue 201.

tools/extract/liftOver_wrapper.py

@@ -5,12 +5,34 @@ Converts coordinates from one build/assembly to another using liftOver binary an
 """
 
 import sys, os, string
+import tempfile
+import re
 
 assert sys.version_info[:2] >= ( 2, 4 )
 
 def stop_err(msg):
     sys.stderr.write(msg)
     sys.exit()
+
+def safe_bed_file(infile):
+    """Make a BED file with track and browser lines ready for liftOver.
+
+    liftOver will fail with track or browser lines. We can make it happy
+    by converting these to comments. See:
+
+    https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html
+    """
+    fix_pat = re.compile("^(track|browser)")
+    (fd, fname) = tempfile.mkstemp()
+    in_handle = open(infile)
+    out_handle = open(fname, "w")
+    for line in in_handle:
+        if fix_pat.match(line):
+            line = "#" + line
+        out_handle.write(line)
+    in_handle.close()
+    out_handle.close()
+    return fname
     
 if len( sys.argv ) != 7:
     stop_err( "USAGE: prog input out_file1 out_file2 input_dbkey output_dbkey minMatch" )
@@ -29,11 +51,15 @@ except:
 if in_dbkey == "?": 
     stop_err( "Input dataset genome build unspecified, click the pencil icon in the history item to specify it." )
 
-cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null 2>&1"
 
 if not os.path.isfile( mapfilepath ):
     stop_err( "%s mapping is not currently available."  % ( mapfilepath.split('/')[-1].split('.')[0] ) )
+
+safe_infile = safe_bed_file(infile)
+cmd_line = "liftOver -minMatch=" + str(minMatch) + " " + safe_infile + " " + mapfilepath + " " + outfile1 + " " + outfile2 + "  > /dev/null 2>&1"
 try:
     os.system( cmd_line )
 except Exception, exc:
-    stop_err( "Exception caught attempting conversion: %s"  % str( exc ) )
+    stop_err( "Exception caught attempting conversion: %s"  % str( exc ) )
+finally:
+    os.remove(safe_infile)

tools/extract/liftOver_wrapper.xml

@@ -42,7 +42,10 @@ Make sure that the genome build of the input dataset is specified (click the pen
 
 .. class:: warningmark
 
-This tool will only work on interval datasets with chromosome in column 1, start co-ordinate in column 2 and end co-ordinate in column 3. If this is not the case with any line of the input dataset, the tool will return empty output datasets.
+This tool will only work on interval datasets with chromosome in column 1,
+start co-ordinate in column 2 and end co-ordinate in column 3. BED comments
+and track and browser lines will be ignored, but if other non-interval lines
+are present the tool will return empty output datasets.
 
 -----