[Biophp-dev] Re: New question from the Newbie

[biophp-dev@bioinformatics.org]

Hello ,

Thanks for your explanation and also for the explanation of the 21 Mar =
2004
concerning how to include a new parser file.
Actually I used the scripts that are on the following urls :
http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/genephp/#dirlist
http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/genephp/parsers/

Am I wrong to use these scripts ?

Do you have an url where I can find updated version of these scripts in =
order
to start playing.

Thanks a lot

Fred



Message: 2
Subject: Re: [Biophp-dev] New question from the Newbie
From: Nico Stuurman <nicos@itsa.ucsf.edu>
To: biophp-dev@bioinformatics.org
Date: 19 Mar 2004 08:18:25 -0800
Reply-To: biophp-dev@bioinformatics.org

Hi Fred,
=20
> I am planning to do a locuslink-file parser.

That is great!  I am quite interested in using that parser!

> So I read the swissprot parser in order to get some good ideas.
> Since my knowledge in php is not as good as yours I have a newbie =
question
> concerning the following line of the function parse_swissprot
>=20
> while (list($no, $linestr) =3D each($flines))

I am a little confused where this code comes from. Did you get the code
from the current biophp cvs (it is all quite confusingly organized at
the moment)?

I am asking, because I can not find a function parse_swissprot.  There
is a class parse_swissprot (in file parsers/swissprot_inc.php).=20
However, this file only contains the line you mention here embedded in a
comment (on line # 167).  Line #166 reads:

while ( list($no, $linestr) =3D each($sourcelines) ) {

$sourcelines is an array that contains every line of the actual data as
an item (in the while loop, $no will hold the line number and $linesrt
the line's content).

Somehow, it looks like you are working with an older version of the
code. =20

It also looks like Sean and I should do a better job documenting how the
parser classes work (I can barely remember myself!).


Hope this helps, please don't hesitate to ask further questions.


Best,

Nico






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