[Biophp-dev] hmmpfam parser

[S Clark]

--nextPart1140506.EzGK2DDuDX
Content-Type: text/plain;
  charset="iso-8859-1"
Content-Transfer-Encoding: 7bit
Content-Disposition: inline

Argh - sorry about the delay in posting - works insane right now...

There actually is already a BLAST xml parser in CVS, though if yours
is better there's no reason we can't change over (for that matter
there's not really any reason we couldn't compare the two and combine them).

If you want to have a look, you can see it in CVS at:

https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/ncbi_blast_parse_xml.inc.php
and the base xml parser from which this class is derived is at:
https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/support_modules/parser_xml.inc.php

Comments and suggestions welcome, as usual.  (I just noticed that although the
frontend class got copied over to the more official "genephp" subdirectory,
the parsers and NCBI-BLAST frontend didn't, apparently - will fix that
later...)

Note that the "parsers" actually interpret the results and contain methods
for fetching the individual result fields as needed.  The whole result in
the form of an associative array (or "hash table" or whatever you want to call
it) is stored by the parser.

If you want to contribute code, just let me know what your login is
at bioinformatics.org and I can add you to the developers list.

Thanks!

Sean

On Friday 09 July 2004 10:42 am, Nico Stuurman wrote:
> Hi Yvan,
>
> You'll first need an account at bioinformatics.org and Sean has to add
> you as a developer.
>
> As for the code itself, we try to adhere the PEAR coding standards
> (http://pear.php.net/manual/en/standards.php).  Not all the code there
> has been PEARified yet, but you can look at biophp/genephp/seq.inc.php
> as an example.  Try to provide ample documentation and references to
> specific algorithms etc. if applicable.
>
> I am not sure where in the structure your parsers would fit (Sean, do
> you have a good idea about this?).  biophp/genephp/parsers is not a
> good idea since these are all parsers for sequence file formats (I
> guess we should rename parsers to importers).
> biophp/genephp/interfaces and biophp/genephp/utilities seem equally
> applicable right now.
>
> In the long run we should get some kind of datastructure holding output
> from blast/fasta like services.  It would be great if you and Sean
> coudl think about that.
>
>
> Hope this helps,
>
>
> Nico
>
> > Just wondering what are the requirements for submiting codes to
> > Biophp? I wrote two parsers for hmmpfam and blast xml outputs, but am
> > afraid they are far from being useable in the context of biophp.
> >
> > Please, could someone explain me the DO and DONT?
> >
> > Regards
> >
> > Yvan
> >
> > _______________________________________________
> > Biophp-dev mailing list
> > Biophp-dev@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biophp-dev
>
> _______________________________________________
> Biophp-dev mailing list
> Biophp-dev@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biophp-dev

--nextPart1140506.EzGK2DDuDX
Content-Type: application/pgp-signature

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.9.9 (GNU/Linux)

iD8DBQBBBXL4J6yQLhNTzSkRAjQZAJsEjpCo3WUewQ5Di15tVk7TvKC9mwCdGmn8
zyN51vqZ+kTHOhG1H56qSMU=
=Ed5S
-----END PGP SIGNATURE-----

--nextPart1140506.EzGK2DDuDX--