[Bioperl-l] Bio::Restriction::IO and REBASE file

[Chris Fields]

Okay, my bad.  Having the format be case-insensitive makes sense and is
probably an easy fix, but there seem to be more serious issues with the
Bio::Restriction::IO modules at the moment.  None have implemented write
methods though POD implies they work:

SYNOPSIS

    use Bio::Restriction::IO;

    $in  = Bio::Restriction::IO->new(-file => "inputfilename" ,
                                     -format => 'withrefm');
    $out = Bio::Restriction::IO->new(-file => ">outputfilename" ,
                                     -format => 'bairoch');
    my $res = $in->read; # a Bio::Restriction::EnzymeCollection
    $out->write($res);

and no tests exist for Bio::Restriction::IO::bairoch yet.  In fact, the
tests are pretty confusing; when did we allow this syntax: '-format => 8'?
Anyway, I'm muddling my way through this and will probably write something
up for the project priority list if I can't work this bug out.  

Chris

> -----Original Message-----
> From: Brian Osborne [mailto:osborne1 at optonline.net]
> Sent: Friday, May 26, 2006 2:43 PM
> To: Chris Fields; 'Jelena Obradovic'; Bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::Restriction::IO and REBASE file
> 
> Chris,
> 
> SeqIO's arguments are case-insensitive (e.g. 'fasta', 'Fasta', 'FASTA'
> should work). This is what the documentation says and what the code seems
> to
> suggest. This is probably what the Restriction modules should do as well.
> 
> Brian O.
> 
>