[Bioperl-l] codon useage modules

[Heikki Lehvaslaiho]

Richard,

Great to see the modules in so soon!

The test script t/DBCUTG.t can not find the cutg example file.
You should run tests like: perl -w t/DBCUTG.t
and the first argument to catfile need to be "t":

ok $db->get_local_request(-file=> Bio::Root::IO->catfile("t", "data",
"MmCT")), 1;

After this test #13 fails.


Rather than having codon table parser inside Bio::DB::CUTG, I think it
would be better to have it in a different module inside Bio::CodonUsage
so that Bio::DB::CUTG need to deal only with web access. Do you think
you could place the IO code in, e.g, Bio::CodonUsage::IO ?

Then we'd have :

Bio::CodonUsage::Table  - codon usage storage object
Bio::CodonUsage::IO     - read and write codon tables
Bio::DB::CUTG           - retrieve codon info from CUTG

Yours,
	-Heikki

On Thu, 2003-09-04 at 13:18, Richard Adams wrote:
> I've committed 2 modules to the CVS using Heikki's suggested namespace:
> 
> Bio::DB::CUTG.pm is for retrieving species specific codon usage tables
> from a web database or from
>         a local file.
>         e.g., my $db = Bio::DB::CUTG->new(-sp => 'Pan troglodytes');
>                        $db->get_web_request();
>                        $db->write_data(-file ">savetolocalfile")
>                            ## get a  Bio::CodonUsage::Table  object:
>                            my $cut = $db->next_data();
> 
> Bio::CodonUsage::Table .pm provides methods on an  objectified Codon
> usage table.
> 
> e.g.,                 $cut->aafrequency() - frequency of that aa in
> organisms proteins
>                         $cut->codon_rel_frequency('CTG') - relative use
> of a particular codon
>                          $cut->get_coding_gc(1)   - GC content of a
> particular codon position
>                             etc.,
> 
> Test script and data also committed.
> 
> Any comments welcome!
> 
> Richard
> 
> --
> Dr Richard Adams
> Bioinformatician,
> Psychiatric Genetics Group,
> Medical Genetics,
> Molecular Medicine Centre,
> Western General Hospital,
> Crewe Rd West,
> Edinburgh UK
> EH4 2XU
> 
> Tel: 44 131 651 1084
> richard.adams at ed.ac.uk
> 
> 
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho    heikki_at_ebi ac uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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