[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.

Bug #3296: newline added in quated features

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

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

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

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

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]=='"':
                        if value[-1]!='"' or value!='"':
                            #No closing quote on the first line...
                            while value[-1] != '"':
-                               value += "\n" + iterator.next() 
+                               value += iterator.next() 
                            #One single line (quoted)
                            assert value == '"'
                            if self.debug : print "Quoted line %s:%s" % (key, value)
                        #DO NOT remove the quotes...

You have received this notification because this email was added to the New Issue Alert plugin

You have received this notification because you have either subscribed to it, or are involved in it.
To change your notification preferences, please click here and login: http://redmine.open-bio.org

More information about the Bioperl-guts-l mailing list