[Bioperl-guts-l] [BioPerl - Bug #3055] GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column

[redmine at redmine.open-bio.org]

Issue #3055 has been updated by Jason Stajich.

Assignee changed from Bioperl Guts to Scott Cain

Scott - can you help check this out to see if it is still a bug?
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Bug #3055: GFF3Loader with allow_whitespace(1) fails to load valid GFF3 with spaces in 9th column
http://redmine.open-bio.org/issues/3055

Author: Nathan Weeks
Status: New
Priority: Normal
Assignee: Scott Cain
Category: Core Components
Target version: main-trunk
URL: 


When invoked with "allow_whitespace(1)", the Bio::DB::SeqFeature::Store::GFF3Loader in bioperl-1.6.1 doesn't handle whitespace in the 9th column.

The following patch seems to fix the issue for our GFF:
##################################################################
--- ./Bio/DB/SeqFeature/Store/GFF3Loader.pm.orig	2010-04-12 11:07:34.000000000 -0500
+++ ./Bio/DB/SeqFeature/Store/GFF3Loader.pm	2010-04-12 11:33:13.000000000 -0500
@@ -497,7 +497,6 @@
   my @columns = map {$_ eq '.' ? undef : $_ } split /\t/,$gff_line;
 
   $self->invalid_gff($gff_line) if @columns < 4;
-  $self->invalid_gff($gff_line) if @columns > 9 && $allow_whitespace;
 
   {
       local $^W = 0;
##################################################################

To save space/time, I've neglected to mention the "symptoms" -- I can provide this information if requested -- but this issue was found by uploading a GFF containing features with the "Target=" attribute into GBrowse 1.70, which sets allow_whitespace(1) for all uploaded GFFs.


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