[Bioperl-l] Fwd: Methods to GenBank

Jason Stajich 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...
http://bioperl.org/wiki/HOWTO:Feature-Annotation#The_Species_Object

Also see the perldoc for Bio::Species or the web Pdoc will tell you  
how to unroll it.
  http://doc.bioperl.org/releases/bioperl-current/bioperl-live/Bio/ 
Species.html

Try something like this:
  my @classification = $species->classification();
  print join("\t", @classification), "\n";


-jason

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  
> Accession.version
>
>   print $seq->species, "\n";
>
> Regards
>
> 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.
>>
>> -jason
>> On Jul 28, 2008, at 1:36 PM, ocar campos wrote:
>>
>>>
>>> Hello:
>>>         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  
>>> Dodds,J.A.
>>>    TITLE     Nucleotide sequence and translation of satellite
>>> tobacco mosaic
>>>             virus RNA
>>>
>>>    And I want to get the Organism part in my script.
>>>
>>>
>>>
>>> Regards
>>>
>>> O'car Campos C.
>>> Estudiante Ingeniería en Bioinformática
>>> Universidad de Talca.
>>>
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