[Biophp-dev] hmmpfam parser

[dong gregorio]

Hi all!

Sorry for being so quiet lately.  I've been rather busy at work.  On the other hand, it's a good thing 'coz some rather interesting ideas have been "incubating" for the time being...

Btw, I met some of the BioPerl "gods" last week... 'twas an interesting encounter... of course, I did my best to plug BioPHP...  =)  

Serge

----- Original Message -----
From: Nico Stuurman <nicos@itsa.ucsf.edu>
Date: Wed, 14 Jul 2004 09:42:02 -0700
To: biophp-dev@bioinformatics.org
Subject: Re: [Biophp-dev] hmmpfam parser

> Hi Yvan,
> 
> That is right.  I was in Ueli Aebi's lab on the third floor between 
> roughly '94 and '98.  Remind me where you were during that time...  
> (and it would be fun to hear what you are doing now in Australia - at 
> least that is what your email address suggests).
> 
> best,
> 
> 
> Nico
> 
> 
> On Jul 11, 2004, at 3:29 PM, yvan wrote:
> 
> > Hi Nico,
> >
> > Thank you for the answer, I will have a look at PEAR.
> >
> > Were you in Basel in the 90th, at the Biocenter, third or fourth 
> > floor? Just wondering your name rings some bells?
> >
> > Cheers
> >
> > Yvan
> >
> >
> > On 10/07/2004, at 2:42 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
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