[Bioperl-l] Re: Sim4

[Ewan Birney]

On Fri, 28 Jul 2000 hilmar.lapp@pharma.novartis.com wrote:

> 
> 
> 
> 
> 
> It is also using the outdated Bio::SeqFeature::Homol. I'll change that to
> the newer Bio::SeqFeature::FeaturePair.
> 
> 
>      Fine. This was my idea, too.
> 
>      There's a little semantic problem left with the notion of Exon for
>      Sim4 alignments and the notion of feature and hit in FeaturePair. For
>      Sim4, you put the shorter sequence first, so that some people might be
>      referring to this as the query. In the FeaturePair object, query will
>      however refer to the sequence having the Exons, that is, the second
>      (genomic) sequence, because you obviously expect
>           $exon_start = $exon->start()
>      return the right result. $exon->hstart() would then return the
>      corresponding coordinate on the 'other' sequence.
> 

Indeed.

>      I'll check that Sim4/Result.pm correctly initializes the Exon object,
>      correctly meaning in the above sense.
> 
>      Then there's still ExonSet which is missing, but I haven't been able
>      to find any special functionality this is supposed to provide. Do you
>      remember the rationale behind this module? Could it be replaced by a
>      2-dimensional array of Exon objects? Or, easier, and maybe more
>      elegant, to handle, an array of Bio::Seq objects (without actual
>      sequences) each having an array of Exon objects as Feature.
> 


I very much dislike the Bio::Seq idea.


>      Another possibility, which I tend to favor: process the Sim4 result in
>      a similar way to multiple sequence files, that is, the user is
>      requested to call repeatedly something like parse_next_alignment(),
>      with each call returning an array of Exon objects.
> 
>      If there are no objections I'll go for that.


sounds good to me.

> 
>           Hilmar
> 
> 
> 
> 
> 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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