[Bioperl-guts-l] [BioPerl - Bug #3296] (New) newline added in quated features

redmine at redmine.open-bio.org redmine at redmine.open-bio.org
Mon Sep 26 16:42:39 EDT 2011


Issue #3296 has been reported by Jesse van Dam.

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Bug #3296: newline added in quated features
https://redmine.open-bio.org/issues/3296

Author: Jesse van Dam
Status: New
Priority: Normal
Assignee: Bioperl Guts
Category: Bio::SeqIO
Target version: 
URL: 


When I have feature line like (which spans multiple lines) 

                     /product="Glutamate synthase [NADPH] small chain (EC 1.4.1
                     .13)"

Then a space/newline will be added between 1.4.1 and .13 in the result so when retrieve the feature with the following code
  print(source[0].qualifiers["product"])

It will print (with the unwanted space) 
Glutamate synthase [NADPH] small chain (EC 1.4.1 .13)

Changed the following thing in scanner.py to fix this problem
                    elif value[0]=='"':
                        #Quoted...
                        if value[-1]!='"' or value!='"':
                            #No closing quote on the first line...
                            while value[-1] != '"':
-                               value += "\n" + iterator.next() 
+                               value += iterator.next() 
                        else:
                            #One single line (quoted)
                            assert value == '"'
                            if self.debug : print "Quoted line %s:%s" % (key, value)
                        #DO NOT remove the quotes...
                        qualifiers.append((key,value))



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