[Bioperl-l] bug fixes

Jason Stajich jason@chg.mc.duke.edu
Mon, 3 Jul 2000 17:37:16 -0400 (EDT)


Fixed on main-trunk and 0.6 branch.
Bio::SeqIO::genbank, Bio::SeqIO::embl, Bio::SeqIO::swiss now reference
$seq->accession_number.

Bio::Seq
$seq->accession now calls $seq->accession_number.

I suppose a deprecation remark is due in there at some point as well to
correct those using Bio::Seq::accession for now it is transparent to the
client.

Also, Bug #243 ( a needed 'use IO::File' in Bio::DB::GenPept) has been
taken care of as well.  Looking to see if more tests can be added to test
all of the methods of implementors of Bio::DB::SeqI.

-Jason
Jason Stajich
Center for Human Genetics
Duke University Medical Center
jason@chg.mc.duke.edu
(919)684-1806 (office)
(919)684-2275 (fax)
http://wwwchg.mc.duke.edu/
On Tue, 4 Jul 2000, Ewan Birney wrote:

> 
> 
> On Mon, 3 Jul 2000, Jason Stajich wrote:
> 
> > We have Bio::Seq::accession and Bio::Seq::accession_number (
> > which accesses Bio::PrimarySeq::accession_number).  But is there really
> > a need for these to be separate?  I expected to run a genbank parser and
> > get data in the $seq->accession_number field for a sequence, but instead
> > saw all unknowns.   Bio::SeqIO::genbank only uses $seq->accession so the
> > data was only accessible through that method.
> 
> This is cruft - Bio::Seq::accession should be shot.
> 
> > 
> > Is this intentional?  Should they point to the same underlying storage
> > instead?  Bio::PrimarySeq::accession_number points to
> > $obj->{'accession_number'} while Bio::Seq::accession points to 
> > $obj->{'accession'}.
> > 
> >  Title   : accession_number
> >  Usage   : $unique_biological_key = $obj->accession_number;
> >  Function: Returns the unique biological id for a sequence, commonly
> >            called the accession_number. For sequences from established
> >            databases, the implementors should try to use the correct
> >            accession number. Notice that primary_id() provides the
> >            unique id for the implemetation, allowing multiple objects
> >            to have the same accession number in a particular
> > implementation.
> > 
> >            For sequences with no accession number, this method should
> > return
> >            "unknown".
> >  Returns : A string
> >  Args    : None
> > 
> >  Title   : accession
> >  Usage   : $obj->accession($newval)
> >  Function: Whilst the underlying sequence object does not 
> >            have an accession, so we need one here. Wont stay
> >            when we do the reimplementation.
> >  Example : 
> >  Returns : value of accession
> >  Args    : newvalue (optional)
> > 
> > 
> > -Jason
> > 
> > Jason Stajich
> > Center for Human Genetics
> > Duke University Medical Center
> > jason@chg.mc.duke.edu
> > (919)684-1806 (office)
> > (919)684-2275 (fax)
> > http://wwwchg.mc.duke.edu/
> > 
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 




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hi,
is any one working on a project using PERL and Drosophila genome . if so may I know some details of it.

2. i  appologize to ask this question ,:

how much capacity one needs in a computer to download the total set of predicted proteins from Drosophila genome .

S.Peri

Bioinfomatics Centre

M.S.Universtiy of Baroda

Baroda INDIA.



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<BR>
<P>hi,
<P>is any one working on a project using PERL and Drosophila genome . if so may I know some details of it.</P>
<P>2. i&nbsp; appologize to ask this question ,:</P>
<P>how much capacity one needs in a computer to download the total set of predicted proteins from Drosophila genome .</P>
<P>S.Peri</P>
<P>Bioinfomatics Centre</P>
<P>M.S.Universtiy of Baroda</P>
<P>Baroda INDIA.</P><p><br><hr size=1><b>Do You Yahoo!?</b><br>
Kick off your party with <a href="http://invites.yahoo.com/">Yahoo! Invites</a>.
--0-719885386-962781422=:19393--

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Date: Wed, 5 Jul 2000 13:17:07 +0100 (BST)
From: Elia Stupka <elia@ebi.ac.uk>
To: Suraj Peri <suraj_peri@yahoo.com>
cc: vsns-bcd-perl@lists.uni-bielefeld.de
Subject: Re: [Bioperl-l] DROSOPHILA +PERL
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Dear Suraj,

You may want to get in contact with the Berkeley Drosophila Genome
Project, who develop open source software for the Drosophila Genome, and a
lot of it is in perl.

Contact them at:
bdgp@fruitfly.berkeley.edu

Elia Stupka

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