[Biophp-dev] hmmpfam parser

[yvan]

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
>>
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