[Bioperl-l] [Bioperl-guts-l] [Bug 1742] New: GFF parser messes attributes (fwd)

[Allen Day]

Here's the stringification problem being discussed in another thread.  It
came up in a 1.5 branch bug report.  Objections to putting the
stringification overload back?

-Allen

---------- Forwarded message ----------
Date: Mon, 31 Jan 2005 15:24:19 -0500
From: bugzilla-daemon at portal.open-bio.org
To: bioperl-guts-l at bioperl.org
Subject: [Bioperl-guts-l] [Bug 1742] New: GFF parser messes attributes

http://bugzilla.open-bio.org/show_bug.cgi?id=1742

           Summary: GFF parser messes attributes
           Product: Bioperl
           Version: 1.5 branch
          Platform: Macintosh
        OS/Version: MacOS X
            Status: NEW
          Severity: major
          Priority: P2
         Component: Core Components
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: jldai at yahoo.com


In BioPerl 1.5.0, use Bio::Tools::GFF and Bio::SeqIO to paser GFF string:

8255763	tigrscan	final-exon	67	558	56.8	-	2	transgrp "1001";

 into an Bio::SeqIO object and later print out as embl file, resulting in:

FT   final-exon      complement(67..558)
FT                   /transgrp="Bio::Annotation::SimpleValue=HASH(0x93a5d8)"
FT                   /note="score=56.8"
FT                   /note="frame=2"

The value of tag "transgrp" should be 1001.

Same script worked fine in BioPerl-1.4



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