[Bioperl-l] sequence object with no sequence data

Nathan Haigh n.haigh at sheffield.ac.uk
Wed Sep 13 12:43:00 EDT 2006


Roy Chaudhuri wrote:
> Hi Nath.
>
> Just a couple more suggestions to add to Hilmar's advice. If you mean
> what I think you do by a "slice", then you may want to look at
> Bio::SeqUtils->trunc_with_features
>
> I don't think it will work correctly without any sequence data, maybe
> you can try creating a sequence consisting of just Ns, by calling
> something like $seq->seq('N'x$seq->length)
>
> As for working with centiMorgan coordinates, couldn't you just
> multiply all your values by a fixed amount (100, say) to give you
> integer coordinates? It might even be possible to hack Bio::Graphics,
> to convert these pseudo-coordinates back into their original format if
> you want to draw a scale etc.
>
> Roy.
> -- 
> Dr. Roy Chaudhuri
> Bioinformatics Research Fellow
> Division of Immunity and Infection
> University of Birmingham, U.K.
>
> http://xbase.bham.ac.uk
Hmm, another excellent idea. The possibility of hacking Bio::Graphics to
display features is definitely once worth considering.

Thanks!
Nath


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