[Bioperl-l] Bio::DB::GenBank new(?) warning

[Smithies, Russell]

What sequence identifiers are you using and what exactly are you trying to get?
Data is available via URL so a simple Perl script will retrieve that:
Eg.
http://eggnog.embl.de/version_3.0/cgi/groupview.py/?group=NOG285349&format=unaligned
http://eggnog.embl.de/version_3.0/cgi/groupview.py/?group=NOG285349&format=newick

I haven't tried it but will Bio::DB::EMBL work?

--Russell

-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of maha ahmed
Sent: Wednesday, 29 August 2012 12:49 p.m.
To: Fields, Christopher J
Cc: Jim Hu; <bioperl-l at bioperl.org>
Subject: Re: [Bioperl-l] Bio::DB::GenBank new(?) warning

Hi guys,
I was searching for a bioperl script I can use to retrieve fasta sequences from the Eggnog database I only found ones to get sequences from Genbank, swissprot or ensembl Did anyone pass by any such script or knows a bioperl module that can be used to retrieve sequences from an online database If not then does anyone know a unix command that can be used to retrieve a sequence from an online database like eggnog

On Tue, Aug 28, 2012 at 10:02 PM, Fields, Christopher J < cjfields at illinois.edu> wrote:

> Is the BioProject DBSOURCE retained if you write the output back using 
> Bio::SeqIO?
>
> chris
>
> On Aug 28, 2012, at 1:09 PM, Jim Hu <jimhu at tamu.edu> wrote:
>
> > I noticed that NCBI recently changed the path to genomes in their 
> > web
> interface. I'm wondering if that's related to my getting this kind of 
> message when I use Bio::DB::GenBank->get_Seq_by_acc()
> >
> > --------------------- WARNING ---------------------
> > MSG: Unrecognized DBSOURCE data: BioProject: PRJNA161931
> >
> > ---------------------------------------------------
> >
> > It still seems to work, though.
> >
> > Jim
> > =====================================
> > Jim Hu
> > Professor
> > Dept. of Biochemistry and Biophysics
> > 2128 TAMU
> > Texas A&M Univ.
> > College Station, TX 77843-2128
> > 979-862-4054
> >
> >
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
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>
>
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