[Biophp-dev] seqdb and seq classes in genephp

[biophp-dev@bioinformatics.org]

On Friday 25 April 2003 09:19 am, nicos@itsa.ucsf.edu wrote:
> [...]I enclose a tar.gz file with the
> code so that you can have a look (don't know if it makes it through teh
> mailing list, not a good idea to include a file, but....)

Postings over 40k currently "pause" in the queue with a message to the list
administrator, who can approve or reject it.  I just approved it, naturally...

I like this idea, though the individual format parsers might end up
being classes themselves (and "enclosed" within the "wrapper" parser
class).

Of course, the really difficult part may be:
> function autodetect () // figures out what seqfiletype this file is,

Then again, that depends on how many different formats we want to be
able to auto-detect.  It may also be worthwhile to have "forced" format
parsing enabled (e.g. the ability to directly call a particular parser without
going through auto-detection, in case auto-detection proves problematic
for some formats).
> function parse_ANSI ()

(Shouldn't that be "ASN.1"?)

I have FASTA and Clustal (.aln) parsers in the module code section already, if
those are helpful at all.

> The SQL stuff could be made self-contained in a similar fashion.  I would
> strongly advice though to stop using the direct MySQL calls but instead
> immediately start using a database abstraction layer like adodb (my
> favorite, I can help out with this one) or PEAR (might finally be usable).

I would personally vote for PEAR, mainly to minimize dependencies on
"non-default" components.  Not that I would MANDATE it, even if I thought
I could get away with it...