[Bioperl-l] http://www.bioperl.org/wiki/Bptutorial.pl

[Mauricio Herrera Cuadra]

Currently I'm modifying the Deobfuscator so it'd be capable of browsing 
the different BioPerl packages as well as their respective releases, but 
haven't got many spare time to finish it :(

Dave and I committed the Deobfuscator into the bioperl-live source tree 
(in /doc directory), so it'd be included in future releases of BioPerl. 
I'm also working on a command line version which won't need a CGI 
environment to have the same functionality, this would address the web 
access situation that you mention.

Phillip SanMiguel wrote:
> Yes I have. It is very useful.
> But in situations where I don't have web access? Or I am working with 
> Bioperl 1.5?
> 
> Mauricio Herrera Cuadra wrote:
>> Hi Philip,
>>
>> Have you tried the Deobfuscator interface? It's a newer and better way 
>> to browse all the methods available in BioPerl:
>>
>> http://bioperl.org/wiki/Deobfuscator
>> http://bioperl.org/cgi-bin/deob_interface.cgi
>>
>> Regards,
>> Mauricio.
>>
>> Phillip SanMiguel wrote:
>>   
>>> Brian Osborne wrote:
>>>     
>>>> Jay,
>>>>
>>>> Excellent! Now we need to answer a few more questions for ourselves:
>>>>
>>>> - Do we remove the file bptutorial.pl from the package now? I'd say yes, we
>>>> don't want to have to maintain two bptutorials.
>>>>   
>>>>       
>>> I would be very disappointed to lose one part of bptutorial.pl--this was 
>>> described in Tisdall's _Mastering Perl for Bioinformatics_. It is the 
>>> only purpose I've ever used bptutorial.pl for--to find all the methods 
>>> available to any given object. Eg:
>>>
>>> bptutorial.pl 100 Bio::PrimarySeq
>>>
>>>  ***Methods for Object Bio::PrimarySeq ********
>>>
>>>
>>>  Methods taken from package Bio::IdentifiableI
>>>  lsid_string   namespace_string
>>>
>>>  Methods taken from package Bio::PrimarySeq
>>>  accession   accession_number   alphabet   authority   can_call_new   desc
>>>  description   direct_seq_set   display_id   display_name   id   is_circular
>>>  length   namespace   new   object_id   primary_id   seq
>>>  subseq   validate_seq   version
>>>
>>>  Methods taken from package Bio::PrimarySeqI
>>>  moltype   revcom   translate   trunc
>>>
>>>  Methods taken from package Bio::Root::Root
>>>  DESTROY   confess   debug   throw   verbose
>>>
>>>  Methods taken from package Bio::Root::RootI
>>>  carp   deprecated   stack_trace   stack_trace_dump   
>>> throw_not_implemented   warn
>>>  warn_not_implemented
>>>
>>>
>>> Phillip SanMiguel
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>     
>>   
> 
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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM