[Bioperl-l] Placement of LargePrimarySeq

Hilmar Lapp hlapp@gmx.net
Mon, 18 Sep 2000 01:32:09 +0200

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