[Bioperl-l] EMBL format field

Marc Logghe Marc.Logghe at ablynx.com
Mon Jun 9 04:47:11 EDT 2008


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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