From 6343c5698e20e6cc210550716e0a43f852024f8a Mon Sep 17 00:00:00 2001
From: Dana Elizabeth Wyman <dwyman@hpc-interactive-1-1.local>
Date: Fri, 28 Sep 2018 15:14:22 -0700
Subject: [PATCH] Fixed bug affecting output of unmapped transcripts to sam
 file

---
 TranscriptClean.py | 1 -
 transcript2.py     | 9 +++++++--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/TranscriptClean.py b/TranscriptClean.py
index 146bc2e..91ec182 100644
--- a/TranscriptClean.py
+++ b/TranscriptClean.py
@@ -690,7 +690,6 @@ def cleanNoncanonical(transcripts, annotatedJunctions, genome, n, spliceAnnot, o
                 Transcript2.addUncorrected_NC_SJ(currTranscript)
 
             else: # Attempt to perform correction
-                print currTranscript.QNAME
                 currSeq = currTranscript.SEQ
                 currCIGAR = currTranscript.CIGAR
                 corrected = []
diff --git a/transcript2.py b/transcript2.py
index 1997b94..e8fde29 100644
--- a/transcript2.py
+++ b/transcript2.py
@@ -295,8 +295,13 @@ def printableSAM(self, genome, spliceAnnot):
         fields = [ self.QNAME, self.FLAG, self.CHROM, self.POS, self.MAPQ, self.CIGAR, \
                    self.RNEXT, self.PNEXT, self.TLEN, self.SEQ, self.QUAL, self.otherFields, \
                    self.NM, self.MD, self.jM, self.jI ]
-        fields = filter(None, fields)
-        return "\t".join([str(x) for x in fields]).strip()
+      
+        final_fields = []
+        for field in fields:
+            if field != "" and field != None:
+                final_fields.append(field)
+        
+        return "\t".join([str(x) for x in final_fields]).strip()
 
     def printableFa(self):
         """ Returns a fasta-formatted string representation of the transcript """