From 532d8e9cd7becf691970b3a7d9e9c618404aaf73 Mon Sep 17 00:00:00 2001
From: Celine Mercier <celine.mercier@metabarcoding.org>
Date: Wed, 4 Oct 2017 15:44:48 +0200
Subject: [PATCH] obi import: small efficiency improvement when dealing with NA
 values

---
 python/obitools3/commands/import.pyx | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx
index 7443149..470cfcf 100644
--- a/python/obitools3/commands/import.pyx
+++ b/python/obitools3/commands/import.pyx
@@ -79,6 +79,7 @@ def run(config):
     cdef   list        old_elements_names
     cdef   list        new_elements_names
     cdef   ProgressBar pb
+    cdef   bytes       NA_value
     global             obi_errno
         
     
@@ -102,6 +103,8 @@ def run(config):
     
     iseq = input[1]
     
+    NA_value = config['obi']['nastring']
+    
     get_quality = False
     NUC_SEQS_view = False
     if isinstance(output[1], View) :
@@ -141,9 +144,9 @@ def run(config):
             if tag != b"ID" and tag != b"DEFINITION" and tag != b"NUC_SEQ" and tag != b"QUALITY" :  # TODO hmmm... 
                                 
                 value = seq[tag]
-                 
+                                
                 # Check NA value
-                if value == config['obi']['nastring'] :
+                if value == NA_value :
                     value = None
                  
                 if tag not in dcols :