[Bioperl-l] Placement of LargePrimarySeq

[Hilmar Lapp]

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.

> 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.

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

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
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