--- a/ensemblref.py	Fri Jan 06 17:43:29 2017 -0500
+++ b/ensemblref.py	Mon Feb 06 09:25:43 2017 -0500
@@ -47,9 +47,15 @@
         return self.name_idx
 
 
-    def get_gtf_transcript(self,transcript_id):
+    def get_gtf_transcript(self,name):
         idx = self.get_transcript_idx()
-        return idx[transcript_id] if transcript_id in idx else None
+        if name in idx:
+            return idx[name]
+        else:
+            nidx = self.get_name_idx()
+            if name in nidx:
+                return nidx[name]
+        return None
 
 
     def transcript_is_coding(self,transcript_id):
@@ -62,34 +68,15 @@
         return tx.start_codons[0] if len(tx.start_codons) > 0 else None
 
 
-    def get_bed_line(self,transcript_id,coding=False):
+    def get_bed_line(self,transcript_id,score=0,itemRgb='0,0,0',coding=False):
         tx = self.get_transcript_idx()[transcript_id]
         chrom = tx.gene.contig
         chromStart = tx.coding_beg if coding else tx.beg 
         chromEnd = tx.coding_end if coding else tx.end
         name = transcript_id
-        score = 0
         strand = '+' if tx.gene.strand else '-'
         thickStart = tx.coding_beg if tx.coding_beg else chromStart
         thickEnd = tx.coding_end if tx.coding_end else chromEnd
-        itemRgb = '0,0,0'
-        exons = tx.get_coding_exons() if coding else tx.get_exons()
-        blockCount = len(exons)
-        if tx.gene.strand:
-            strand = '+'
-            blockSizes = [abs(e-s) for s,e in exons]
-
-    def get_bed_line(self,transcript_id,coding=False):
-        tx = self.get_transcript_idx()[transcript_id]
-        chrom = tx.gene.contig
-        chromStart = tx.coding_beg if coding else tx.beg 
-        chromEnd = tx.coding_end if coding else tx.end
-        name = transcript_id
-        score = 0
-        strand = '+' if tx.gene.strand else '-'
-        thickStart = tx.coding_beg if tx.coding_beg else chromStart
-        thickEnd = tx.coding_end if tx.coding_end else chromEnd
-        itemRgb = '0,0,0'
         exons = tx.get_coding_exons() if coding else tx.get_exons()
         blockCount = len(exons)
         if tx.gene.strand: