[Biophp-dev] [Biophp-dev]matrices scores (was:Re: levenshtein distance)

[S Clark]

On Sunday 25 May 2003 03:14 pm, Serge Gregorio wrote:
>  how useful is a "writer" module (opposite of
> "parser")? When do users need to output their data in a specific format
> (eg. GenBank)?

Two situations - when people are processing data to give to someone else, and
when generating data for export to another program (e.g. fastDNAml, Clustal,
etc.)

If nothing else, it'll be useful to be able to save data collected and
generated in PHP in a relatively "neutral" format (e.g. Genbank for sequences, 
Clustal for alignments) for processing later, even if for no other reason than
to avoid needing to invent a new BioPHP-specific format (though we might do
that, too, at some point if we want to.)

> Sean, any news re: eFetch/eUtils?  Haven't touched the folder you set aside
> for the psscan perl script yet...

Nothing new to report there yet - if I can get the Universe to quit pestering
me for an hour I can get the ESearch and ESummary modules properly split
up (nothing substantial needed in terms of coding, just moving
bits into separate files and adding and "include_once()" to each).

I'm CURRENTLY planning to tackle EFetch for nucleotide and then protein
sequences just after the NCBI Blast interface is up to its initial
usable state - if there's a more urgent need for EFetch there's no reason
I can't start on it first, though.

Oh, yes, and Welcome Back!

Sean