From 3ffb34a41c7a0f91b5915c5db2860bc4e9a7e68c Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Fri, 9 Mar 2007 19:54:46 +0000
Subject: [PATCH] Fix for displaying BED6+ at UCSC.

---
 lib/galaxy/datatypes/interval.py | 30 ++++++++++++++++++++++++++++++
 lib/galaxy/interfaces/root.py    |  4 +---
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/datatypes/interval.py b/lib/galaxy/datatypes/interval.py
index 855652675d5..890937429da 100644
--- a/lib/galaxy/datatypes/interval.py
+++ b/lib/galaxy/datatypes/interval.py
@@ -197,6 +197,36 @@ class Bed( Interval ):
     def set_meta( self, dataset ):
         # metadata already set
         pass
+    def as_bedfile( self, dataset ):
+        '''Returns a file that contains only the bed data. If bed 6+, treat as interval.'''
+        for line in open(dataset.file_name):
+            line = line.strip()
+            if line == "" or line.startswith("#"): continue
+            fields = line.split('\t')
+            #check to see if this file doesn't conform to strict genome browser accepted bed
+            try:
+                if len(fields)>12: return Interval.as_bedfile(self, dataset) #too many fields
+                if len(fields)>6:
+                    if len(fields) > 6:
+                        int(fields[6])
+                        if len(fields) > 7:
+                            int(fields[7])
+                            if len(fields) > 8:
+                                if int(fields[8]) != 0: return Interval.as_bedfile(self, dataset)
+                                if len(fields) > 9:
+                                    int(fields[9])
+                                    if len(fields) > 10:
+                                        fields2 = fields[10].rstrip(",").split(",") #remove trailing comma and split on comma
+                                        for field in fields2: int(field)
+                                        if len(fields) > 11:
+                                            fields2 = fields[11].rstrip(",").split(",") #remove trailing comma and split on comma
+                                            for field in fields2: int(field)
+            except: return Interval.as_bedfile(self, dataset)
+            #only check first line for proper form
+            break
+            
+        try: return dataset.file_name
+        except: return "This item contains no content"
 
 class Gff( Tabular ):
     """Tab delimited data in Gff format"""
diff --git a/lib/galaxy/interfaces/root.py b/lib/galaxy/interfaces/root.py
index b4618625b46..0581a91cf49 100644
--- a/lib/galaxy/interfaces/root.py
+++ b/lib/galaxy/interfaces/root.py
@@ -117,9 +117,7 @@ class Universe(common.Root):
         """Returns a bed file"""
         data = self.app.model.Dataset.get( id )
         if data:
-            if isinstance(data.datatype, datatypes.interval.Bed):
-                return self.display(trans, id=data.id)
-            elif isinstance(data.datatype, datatypes.interval.Interval):
+            if isinstance(data.datatype, datatypes.interval.Interval):
                 mime = data.get_mime()
                 trans.response.set_content_type(mime)
                 file_name = data.as_bedfile()