+ extended manual to describe output file format

[qpalma.git] / qpalma / OutputFormat.py

diff --git a/qpalma/OutputFormat.py b/qpalma/OutputFormat.py
index 85c41cd..6e3a1f4 100644 (file)
--- a/qpalma/OutputFormat.py
+++ b/qpalma/OutputFormat.py
@@ -245,8 +245,8 @@ def createBlatOutput(current_prediction,settings):
    gaps  = exonGaps
    gaps  = [int(elem) for elem in gaps]
 
-   new_line = '%d\t%d\t%s\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' %\
-   (id,chromo,strand,seq,start_pos,qStart,qEnd,tStart,tEnd,num_exons,\
+   new_line = '%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' %\
+   (id,chromo,strand,start_pos,qStart,qEnd,tStart,tEnd,num_exons,\
    pp(qExonSizes),pp(qStarts),pp(qEnds),pp(tExonSizes),\
    pp(tStarts),pp(tEnds),pp(ids),pp(gaps))