[Bioperl-l] Re: Bio::DB::Query

[Hilmar Lapp]

Carito,

sorry I didn't have time to get back to you earlier. The documentation 
of many modules is certainly far from complete, and most if not all 
modules could certainly benefit a lot from examples. The fact that 
documentation is sparse in many cases is not due to ignorance or 
oversight though, but simply due to lack of time, or in other words 
lack of volunteers.

As for modifying records after they are read by SeqIO and before they 
are stored in the database, the perfect mechanism for this with support 
built into load_seqdatabase.pl is to write a sequence processor. Have 
you read the documentation under the --pipeline option in 
load_seqdatabase.pl? It references the respective modules in bioperl 
that the framework is built upon which will have more documentation. I 
use this every day with great success for my own projects.

As for the rest of your email, be sure to note one thing. 
Bioperl/biosql/bioperl-db is open source - you didn't pay for it, did 
you? - and has been written by volunteers, i.e., people who didn't stop 
at complaining but went on to volunteer their unpaid time and made this 
world a better place for themselves and everybody else too by making an 
effort to correct the issues they found.

	-hilmar

On Thursday, April 21, 2005, at 12:57  PM, carito vargas wrote:

> Hi
>
>> Bio::DB::Query::BioQuery will map classes to tables for you. There's 
>> no
>> really good HowTo document yet; there's plenty of examples though in
>> the respective test script t/query.t.
>
> It should be good that in that in the bioperl API appear examples,
> there are many functions with nothing of documentation...
>
>> I don't understand your goal in modifying load_seqdatabase.pl, so
>> unless you elaborate on what you're trying to achieve I can't help 
>> you.
>
> My goal for modifying load_seqdatabase.pl is because I wanted to store
> different .gbk files but with few modifications, and we needed to
> store them all with different versions.... I could have done it by
> using ohter parsing aplication before...
>
> thank you ..
>
> carito
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------