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

Phillip SanMiguel pmiguel at purdue.edu
Sat Jun 24 12:59:21 EDT 2006


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
>>
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>     
>
>   



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