[Biophp-dev] hmmpfam parser

[Nico Stuurman]

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
>