[Biophp-dev] hmmpfam parser

[Nico Stuurman]

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
>>>
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>>
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