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

[Jelena Obradovic]

Hi guys, I tried with the other formats, and it works fine with "withrefm"
format but not with "withref".

Thanks a lot for your reponse.

Cheers,

Jelena

On 5/26/06, Chris Fields <cjfields at uiuc.edu> wrote:
>
>
>
> > -----Original Message-----
> > From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> > bounces at lists.open-bio.org] On Behalf Of Jelena Obradovic
> > Sent: Friday, May 26, 2006 11:47 AM
> > To: Bioperl-l at lists.open-bio.org
> > Subject: [Bioperl-l] Bio::Restriction::IO and REBASE file
> >
> > Hi there,
> >
> > I have tried loading enzyme list from a file REBASE bairoch.605 using
> > Bio::Restriction::IO;
> >
> > 1. But for some reason the number of enzymes in the list is always 532
> > which is a default set of enzymes in enzyme collection.
> >
> > Is there any known issue with this module or a workaround?
> >
> > And here is the code I have been using:
> >
> > my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
> > format=>"Bairoch")
> > || die "can't load the file bairoch.605: $!";
> > my $enzymes = $re_in->read;
> > print "\nNo of enzymes: ", scalar $enzymes->each_enzyme, "\n";
>
> my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
>                                    format=>"Bairoch");
>
> should be
>
> my $re_in=Bio::Restriction::IO->new(-file=>"bairoch_605.dat",-
>                                    format=>"bairoch");
>
> Note the case change for the format; this is noted in the bug report you
> submitted earlier.  Bio::Restriction::IO works similarly to Bio::SeqIO (
> i.e.
> requires a specific format, which I believe is case-sensitive).  Judging
> by
> the modules in Bio/Restriction/IO directory, looks like the
> Bio::Restriction::IO format should match one of the following formats:
> bairoch, itype2, withrefm, and you can also build your own if needed using
> the previous as examples and implementing Bio::Restriction::IO::base.
>
> > 2. The other problem is when trying to use format that is lower-case
> > it throws an exception, but when "B" is capitalized it is ok.
> > I assume it cannot load a file and does not initilize enzyme
> > collection properly.
> >
> > Can't call method "each_enzyme" on an undefined value at
> > .../cgi-bin/seq-load.pl line 51.
>
> My guess?  The reason it works with an uppercase ('Bairoch') is that it
> can't find the module and uses the default set of enzymes as a fallback.
> The exception that you reported when you use lowercase ('bairoch') is real
> and I reported it as a bug (there are a few I found in that module).
>
> You might want to try using one of the other formats if you can get the
> files in the right format from REBASE.  I'm looking into the bugs
> specifically associated with Bio::Restriction::IO::bairoch.
>
> > Any thoughts?
> >
> >
> > Thanks in advance,
> >
> >
> > Jelena Obradovic
> > jelenaob at gmail.com
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>


-- 
Jelena Obradovic
Email: jobradovic at gmail.com