[Bioperl-l] Fwd: Methods to GenBank

ocar campos ocar1987 at hotmail.com
Mon Jul 28 17:39:35 EDT 2008


Thanks for the help, got what i wanted.

$gb = new Bio::DB::GenBank();
$seq = $gb->get_Seq_by_version('M25782.1');

 $species=$seq->species;
 print $species->common_name, "\n";
 print $species->species, "\n";
 print $species->genus, "\n";
 print $species->sub_species, "\n";
 print $species->binomial, "\n";
 print $species->ncbi_taxid, "\n";

O'car

----------------------------------------
> From: jason at bioperl.org
> Date: Mon, 28 Jul 2008 14:16:22 -0700
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Fwd:  Methods to GenBank
> 
> 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 
>> Date: July 28, 2008 2:05:46 PM PDT
>> To: Jason Stajich 
>> 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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