[Bioperl-l] SimpleAlign Ids

Mark A. Jensen maj at fortinbras.us
Thu Apr 22 17:42:00 EDT 2010

Hi Bernd,
I'm for the idea of an internal uid for sequences; tree nodes already work like 
this, for example, and I think it's the Right Thing To Do.
----- Original Message ----- 
From: "Bernd Web" <bernd.web at gmail.com>
To: "BioPerl List" <bioperl-l at bioperl.org>
Sent: Wednesday, April 21, 2010 1:08 PM
Subject: [Bioperl-l] SimpleAlign Ids

> Hi
> Would it be an idea to change SimpleAlign/AlignIO as not to use
> sequence IDs in the hash to store the sequences?
> Quite regularly I run into issues with alignments that do not have
> unique IDs. This esp. occurs with alignments from the CDD at NCBI.
> When I know the input format I (or a user) is using, I have a
> pre-processing step to make all IDs unique.
> However, when the input format can change everytime, it is really
> handy to use SimpleAlign with the format guesser.
> When the sequence objects would be stored using unique keys instead of
> Ids this issue would not occur.
> I can image that for other using large alignments this might not be
> handy as I suppose an extra lookup step would be needed.
> Is the above an issue that  others run into too?
> Kind regards,
> Bernd
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