[Biojava-dev] Parsing PfamScan results

[Jules Jacobsen]

Is this the stockholm format you're talking about? If so I've partly 
written one for BioJava3 although came a bit unstuck with the multiple 
sequence alignment sequence and the new Sequence class.

I need to reply to Scooter and Andy's thread regarding the Sequence 
stuff though.

Sorry - got to get the bus now...!

Jules


On 04/05/2010 01:30, Andreas Prlic wrote:
> sure, just  post the code here, we can do a review...
>
> Andreas
>
> On Sun, May 2, 2010 at 9:59 PM, Radwen Aniba<aradwen at gmail.com>  wrote:
>
>> Hi Anreas,
>>
>> Yes I've parsed Biojava API looking for something like that but started to
>> write my own parser in Java, may be if someone could need it I can write a
>> message with a code here.
>>
>> Thx anyway
>>
>> Rad
>>
>> 2010/5/3 Andreas Prlic<andreas at sdsc.edu>
>>
>> Hi Radwen,
>>>
>>> So far there is no PfamScan parser in BioJava....
>>>
>>> Andreas
>>>
>>> On Sat, May 1, 2010 at 2:42 AM, Radwen Aniba<aradwen at gmail.com>  wrote:
>>>
>>>> Hi everyone,
>>>>
>>>> Do anyone already tried to implement a method to parse PfamScan outputs ?
>>>> That's not too hard to do but I'm planning to write it in Java, but
>>>> before I
>>>> ignore if this is possible with Biojava or if someone already did
>>>> somthing
>>>> in that sense, it would be helpful.
>>>>
>>>> Regards
>>>>
>>>> Radwen
>>>>
>>>> --
>>>> R. ANIBA
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>
>>>
>>>
>>>
>>> --
>>> -----------------------------------------------------------------------
>>> Dr. Andreas Prlic
>>> Senior Scientist, RCSB PDB Protein Data Bank
>>> University of California, San Diego
>>> (+1) 858.246.0526
>>> -----------------------------------------------------------------------
>>>
>>
>>
>>
>> --
>> R. ANIBA
>>
>> Bioinformatics PhD
>> Laboratoire de Bioinformatique et Génomique Intégratives,
>> Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC),
>> 1 rue Laurent Fries,
>> 67404 Illkirch, France.
>> http://www-igbmc.u-strasbg.fr
>> http://alnitak.u-strasbg.fr/~aniba/alexsys<http://alnitak.u-strasbg.fr/%7Eaniba/alexsys>
>>
>
>
>