[Bioperl-l] EMBL format field

Wen Huang whuang.ustc at gmail.com
Mon Jun 9 10:05:35 EDT 2008


Hi Marc,

Thanks a lot! It does work!!

Wen
On Jun 9, 2008, at 3:47 AM, Marc Logghe wrote:

> Hi Wen,
> A dump of that sequence object (Data::Dumper is your friend !) reveals
> that the PA EMBL field is not saved into the object. However, you will
> find the string 'AB000170.1' in the embedded CDS feature, more  
> precisely
> the seqid of the location object. I don't know whether that is always
> the case, but it is in your particular example.
> So, to get your hands on that value you have to do:
>
> my ($cds) = grep {$_->primary_tag eq 'CDS'} $seq->get_SeqFeatures;
> my $parent_id = $cds->location->seq_id;
>
> HTH,
> Marc
>
> Marc Logghe
> Senior Bioinformatician
> Ablynx nv
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Wen Huang
>> Sent: Monday, June 09, 2008 5:28 AM
>> To: bioperl-l at lists.open-bio.org
>> Subject: [Bioperl-l] EMBL format field
>>
>> Hi all,
>>
>> I have a EMBL file that I want to extract one of the line
>>
>> ###file###
>> ID   BAA19060; SV 1; linear; mRNA; STD; MAM; 2115 BP.
>> XX
>> PA   AB000170.1
>> XX
>> DE   Sus scrofa (pig) endopeptidase 24.16 type M1
>> XX
>> OS   Sus scrofa (pig)
>> OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;  
>> Euteleostomi;
>> Mammalia;
>> OC   Eutheria; Laurasiatheria; Cetartiodactyla; Suina; Suidae; Sus.
>> OX   NCBI_TaxID=9823;
>> .........
>>
>> I want the accession number in the line that starts with PA, AB000170
>> in this example.
>>
>> Can anybody kindly help, tell me which module and method I should  
>> use?
>> I tried various things like $seq_obj -> primary_id, display_id,
>> get_secondary_id, etc.. they did not work...
>>
>> Thanks a lot!
>>
>> Wen
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