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

Chris Fields cjfields at uiuc.edu
Sat Jun 24 15:07:06 EDT 2006


As a quickie method I use the script from the FAQ; you have to  
install Class::Inspector:

#!/usr/bin/perl -w
use Class::Inspector;
$class = shift || die "Usage: methods perl_class_name\n";
eval "require $class";
print join ("\n", sort @{Class::Inspector->methods 
($class,'full','public')}), "\n";

Works well, though doesn't have the links and so on like  
Deobfuscator; I use HTML-generated ActiveState docs:

glaciers-115 chris$ methods.pl Bio::SeqIO
Bio::Root::IO::catfile
Bio::Root::IO::close
Bio::Root::IO::dup
Bio::Root::IO::exists_exe
Bio::Root::IO::file
Bio::Root::IO::flush
Bio::Root::IO::gensym
Bio::Root::IO::mode
Bio::Root::IO::noclose
Bio::Root::IO::qualify
Bio::Root::IO::qualify_to_ref
Bio::Root::IO::rmtree
Bio::Root::IO::tempdir
Bio::Root::IO::tempfile
Bio::Root::IO::ungensym
Bio::Root::Root::debug
Bio::Root::Root::except
Bio::Root::Root::finally
Bio::Root::Root::otherwise
Bio::Root::Root::throw
Bio::Root::Root::try
Bio::Root::Root::verbose
Bio::Root::Root::with
Bio::Root::RootI::carp
Bio::Root::RootI::confess
Bio::Root::RootI::deprecated
Bio::Root::RootI::stack_trace
Bio::Root::RootI::stack_trace_dump
Bio::Root::RootI::throw_not_implemented
Bio::Root::RootI::warn
Bio::Root::RootI::warn_not_implemented
Bio::SeqIO::DESTROY
Bio::SeqIO::PRINT
Bio::SeqIO::READLINE
Bio::SeqIO::TIEHANDLE
Bio::SeqIO::alphabet
Bio::SeqIO::fh
Bio::SeqIO::location_factory
Bio::SeqIO::new
Bio::SeqIO::newFh
Bio::SeqIO::next_seq
Bio::SeqIO::object_factory
Bio::SeqIO::sequence_builder
Bio::SeqIO::sequence_factory
Bio::SeqIO::write_seq


Chris

On Jun 24, 2006, at 12:48 PM, Phillip SanMiguel wrote:

>
> 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
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>>
>>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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