Mercurial > repos > bornea > saint_preprocessing

changeset 54:0f5028e0c39c draft

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Uploaded
author bornea
date Sat, 27 Aug 2016 20:25:34 -0400
parents 26b5bd96332e
children 340cc5988c31
files SAINT_preprocessing_mq_pep.py
diffstat 1 files changed, 3 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/SAINT_preprocessing_mq_pep.py	Sat Aug 27 20:25:09 2016 -0400
+++ b/SAINT_preprocessing_mq_pep.py	Sat Aug 27 20:25:34 2016 -0400
@@ -145,6 +145,7 @@
     db_len = len(data_lines)
     seqlength = 0
     count = 0
+    last_line = data_lines[-1]
     for data_line in data_lines:
         if ">sp" in data_line:
             if uniprot_accession_in == data_line.split("|")[1]:
@@ -158,6 +159,8 @@
                 while ">sp" not in data_lines[match]:
                     if match <= db_len:
                         seqlength = seqlength + len(data_lines[match].strip())
+                        if data_lines[match] == last_line:
+                            break
                         match = match + 1
                     else:
                         break
@@ -264,7 +267,6 @@
         if seq != 'NA':
             if GN != 'NA':
                 valid_prots.append(a)
-    print valid_prots
     with open('inter.txt', 'w') as input_file:
         l = 0; a = 0
         for bb in bait: