[Bioperl-l] Placement of LargePrimarySeq

[Ewan Birney]

On Mon, 18 Sep 2000, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > 
> > I have this object as Bio::LargePrimarySeq. Does anyone have any
> > objections about having this object in the Bio:: area directly or should
> > I put it somewhere else (bascially, what do people feel about cluttering
> > up the top level Bio:: area, or should I make a Bio::Seq:: directory.
> 
> Basically, I'd reserve Bio:: for modules which are rather basic, and
> avoid cluttering with specialized classes deriving others. LocatableSeq
> could go under Bio::Seq::, too.

ok. I'll make a Bio::Seq for all the sequence ish extensions.

> 
> > NB - there might be some other extensions, like Bio::CachePrimarySeq which
> > can cache subseq calls to improve performance for LargePrimarySeq and
> > the Ensembl database equivalents...)
> 
> These should really better go under their own directory, shouldn't they?
> 
> > 
> > I need to write a SeqIO system for making this and also writing out very
> > large fasta files. (it should step through the sequence one MB at a time
> > using the subseq method, rather than getting the whole thing out as a
> > seq). Options:
> > 
> >         (a) make a new Bio::SeqIO::bigfasta module, and ->next_seq would
> > make sequences with LargePrimarySeq and ->write_seq would write with
> > this subseq method
> > 
> >         (b) parameterise Bio::SeqIO::fasta for both of these. (have to
> > handle boring don't use $/ stuff as reading can't put everything between
> > '>' as a string, as the whole point is not to have the entire sequence as
> > a string in memory)
> > 
> > I prefer (a) to (b).
> > 
> 
> So do I.
> 

cool.

> BTW I'm sure you know that some people appear to be using bioperl under
> Windows. So, temp directory determination etc should be compatible.
> 

great. Do you happen to know how to do that? Is there a perl call for
"give me a temp directory"


> 	Hilmar
> 
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
> -----------------------------------------------------------------
> 

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