Mercurial > repos > johnheap > vapper

diff Tryp_T.py @ 4:8f6469ffef85 draft

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planemo upload for repository https://github.com/johnheap/VAPPER-Galaxy
author johnheap
date Thu, 19 Jul 2018 06:38:58 -0400
parents 36cb22bd911d
children 25226d33642e
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line diff
--- a/Tryp_T.py	Wed Jul 11 08:58:14 2018 -0400
+++ b/Tryp_T.py	Thu Jul 19 06:38:58 2018 -0400
@@ -89,7 +89,7 @@
     if strain == "Tc148":
         refName = dir_path + "/data/Reference/148_prot.fasta"
     if strain == "IL3000":
-        refName = dir_path + "data/Reference/IL3000_prot.fasta"
+        refName = dir_path + "/data/Reference/IL3000_prot.fasta"
 
     cuff_df = pd.read_csv(inputName+".cuff/genes.fpkm_tracking", sep='\t')
     cuff_df = cuff_df[(cuff_df['FPKM'] > 0)]
@@ -124,6 +124,8 @@
                         while line[0] != '>':
                             outfile.write(line)
                             line=ref.readline()
+                            if not line:
+                                break;
                 else:
                     line = ref.readline()
             else: