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

[Hilmar Lapp]

This is coming from SeqFeature::Annotated, right? What's wrong with 
making SeqFeature::Annotated return a tag's value as a string as 
demanded by the contract instead of returning an object?

IMNSHO stringification overload band-aids rather than fixes the 
problem, and also introduces a trip wire that sooner or later will be 
triggered by someone unsuspecting. I.e., it makes the code more 
brittle, not more robust. You won't like me for this, but I do think 
it's the wrong strategy.

	-hilmar

On Jan 31, 2005, at 2:27 PM, Allen Day wrote:

> 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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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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