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

Phillip SanMiguel pmiguel at purdue.edu
Sat Jun 24 13:48:15 EDT 2006


Yes, that would be better than bptutorial.pl 100 then. For some modules 
bptutorial.pl 100 doesn't seem to give any of the methods they have 
access to. Whereas the deobfuscator does.

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