[Bioperl-l] Fwd: Methods to GenBank
jason at bioperl.org
Mon Jul 28 17:16:22 EDT 2008
Please respond to the list with any queries.
It is a Bio::Species object
You might try and "Search" for species on the wiki and you'll find a
lot of already written info...
Also see the perldoc for Bio::Species or the web Pdoc will tell you
how to unroll it.
Try something like this:
my @classification = $species->classification();
print join("\t", @classification), "\n";
Begin forwarded message:
> From: ocar campos <ocar1987 at hotmail.com>
> Date: July 28, 2008 2:05:46 PM PDT
> To: Jason Stajich <jason at bioperl.org>
> Subject: RE: [Bioperl-l] Methods to GenBank
> I've been looking in the Seq How To but I haven't found it.... this
> is what i got.
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> $gb = new Bio::DB::GenBank();
> $seq = $gb->get_Seq_by_version('M25782.1'); # Get sequence by
> print $seq->species, "\n";
> O'car Campos
>> From: jason at bioperl.org
>> Date: Mon, 28 Jul 2008 13:45:42 -0700
>> To: ocar1987 at hotmail.com
>> CC: bioperl-l at lists.open-bio.org
>> Subject: Re: [Bioperl-l] Methods to GenBank
>> you want the species method.
>> see the Seq HowTo on the bioperl wiki -> bioperl.org/wiki for more
>> detailed info on how to get all the fields out from a seq object.
>> On Jul 28, 2008, at 1:36 PM, ocar campos wrote:
>>> I'm building a script to get information from GenBank
>>> according to some Accession Id, I've looked for a method to
>>> retrieve the organism lines from the GenBank, but i haven't found
>>> any specific for this. Does anyone know what is the method for this?
>>> For example i got this GenBank File:
>>> LOCUS SLLCP 1058 bp ss-RNA linear
>>> VRL 16-AUG-1994
>>> DEFINITION Satellite tobacco mosaic virus coat protein RNA,
>>> complete cds.
>>> ACCESSION M25782
>>> VERSION M25782.1 GI:530201
>>> KEYWORDS coat protein.
>>> SOURCE Tobacco necrosis satellite virus
>>> ORGANISM Tobacco necrosis satellite virus
>>> Viruses; Satellites; Satellite Viruses.
>>> REFERENCE 1 (bases 1 to 1058)
>>> AUTHORS Mirkov,T.E., Mathews,D.M., Du Plessis,D.H. and
>>> TITLE Nucleotide sequence and translation of satellite
>>> tobacco mosaic
>>> virus RNA
>>> And I want to get the Organism part in my script.
>>> O'car Campos C.
>>> Estudiante Ingeniería en Bioinformática
>>> Universidad de Talca.
>>> News, entertainment and everything you care about at Live.com. Get
>>> it now!
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>>> Bioperl-l at lists.open-bio.org
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