[Biophp-dev] BLAST parser

[S Clark]

There is also one that I wrote, that is in the BioPHP CVS.  I don't know if 
the way I implemented it will appeal to anyone else, but comments are 
welcome.  It's used by the two BLAST frontends (one for the NCBI API online, 
another for running a local copy of blast).

The needed files are in CVS here:

https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/frontend_blast.php
https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/ncbi_url_blast.inc.php
https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/ncbi_blast_parse_xml.inc.php
https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/support_modules/parser_xml.inc.php
https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi-official/support_modules/postbox_class.php

(I believe that's all of them - it's been a very hectic last nearly-two-years 
and I've not had time to look at them much in the meantime...)

Note that Nico also wrote an XML parser class (to go with his elink interface) 
which I haven't had a chance to look at, but I suspect is probably a lot 
simpler to use than mine - mine was designed with the intention of being very 
portable (to use, just "extend" my core class into a class specific to the 
type of XML data you're parsing) but is still somewhat laborious to use due 
to what is probably a somewhat heavy-handed yet amateur "Object Oriented" 
design (focus on using "interface methods" instead of direct access to the 
data values means defining functions for each data field that you want to 
retrieve...)

As always, comments and suggestions welcome.

On Saturday 05 March 2005 11:21 am, Yvan Strahm wrote:
> Hello Andrés,
>
> I wrote one which work with php4 and use the expat library. As i am
> using it to enter the results into a database, you will have to change
> it a little bit to make it work as standalone. Tell me if you want
> have a look at it.
>
> Cheers
> Yvan
>
> On Sat, 5 Mar 2005 09:30:27 -0500, Andres Pinzon <andrespinzon at gmail.com> 
wrote:
> > Hi,
> > Im working on a PHP XML parser for blast results ("-m 7" option). I
> > used to work with html4blast, but i decided to write one of my own, i
> > need it because i work with the sib's blast client-server and the
> > blastall.remote retrieves the query in a ugly ascii form.
> > Before starting i would like to know if you have worked on something
> > similar. Thanks!
> > --
> > ---------
> > Andrés Pinzón [http://www.andrespinzon.com]
> > Centro de Bioinformatica, Instituto de Biotecnologia
> > Universidad Nacional de Colombia
> > GNU/Linux ...para un mundo libre!
> > ----------
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