[Bioperl-l] simple PrimarySeq question

[niels at genomics.dk]

Kevin,

Thanks, but I didnt put the question very clearly sorry .. yes, SeqIO
gets entries from file, and from those large parsed entries I can get a
simplified primary_seq object. But the SeqIO object includes feature
and annotation objects etc that takes time to make, and I wish to know
if there is a way to get a primari_seq object without this overhead. I
apologize if I overlooked it in the docs.

Niels




> Start by having a look at the following link:
> http://bioperl.org/cgi-bin/deob_interface.cgi
>
> SeqIO is how one reads or writes sequences to/from files.
> Bio::PrimarySeq is just an object that holds information about a
> sequence obtained from a file.
>
> As for how to parse a Genbank file into a list of features:
>
> $file = Bio::SeqIO->new(-format => $format, -file => "id.gb");
> while (my $seq = $file->next_seq())
> {
> 	@features = $seq->all_SeqFeatures;
> 	# sort features by their primary tags
> 	for my $f (@features)
> 	{
> 		my $tag = $f->primary_tag;
> 		if ($tag eq 'CDS')
> 		{
> 			# @sorted_features holds all the Bio::PrimarySeq
> features obtained from the genbank file
> 			push @sorted_features, $f;
> 		}
> 	}
> }
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org
>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> Niels Larsen
>> Sent: Monday, July 02, 2007 1:45 PM
>> Cc: bioperl-l List
>> Subject: [Bioperl-l] simple PrimarySeq question
>>
>> I write hoping someone could show me how to create a
>> PrimarySeq object without parsing features and all first. The
>> lines below return
>>
>> "Can't locate object method "next_seq" via package
>> "Bio::PrimarySeq" at ./tst2 line 16."
>>
>> whereas calling Bio::SeqIO-> gives no error, but a too big object.
>> The GenBank record after the __END__ is the "1.gb" file. I
>> could not find out how from the tutorial or the
>> Bio::PrimarySeq description.
>>
>> Niels L
>>
>>
>> #!/usr/bin/env perl
>>
>> use strict;
>> use warnings FATAL => qw ( all );
>>
>> use Data::Dumper;
>>
>> use Bio::Seq;
>> use Bio::SeqIO;
>>
>> my ( $seq_h, $seq );
>>
>> $seq_h = Bio::PrimarySeq->new( -file => "1.gb", -format =>
>> 'genbank' ); # $seq_h = Bio::SeqIO->new( -file => "1.gb",
>> -format => 'genbank' );
>>
>> $seq = $seq_h->next_seq();
>>
>> # print Dumper( $seq );
>>
>> __END__
>>
>> LOCUS       X60065                     9 bp    mRNA    linear
>>   MAM 14-NOV-2006
>> DEFINITION  B.bovis beta-2-gpI mRNA for beta-2-glycoprotein I.
>> ACCESSION   X60065 REGION: 1..9
>> VERSION     X60065.1  GI:5
>> KEYWORDS    beta-2 glycoprotein I.
>> SOURCE      Bos taurus (cattle)
>>    ORGANISM  Bos taurus
>>              Eukaryota; Metazoa; Chordata; Craniata;
>> Vertebrata; Euteleostomi;
>>              Mammalia; Eutheria; Laurasiatheria;
>> Cetartiodactyla; Ruminantia;
>>              Pecora; Bovidae; Bovinae; Bos.
>> REFERENCE   1
>>    AUTHORS   Bendixen,E., Halkier,T., Magnusson,S.,
>> Sottrup-Jensen,L. and
>>              Kristensen,T.
>>    TITLE     Complete primary structure of bovine beta
>> 2-glycoprotein I:
>>              localization of the disulfide bridges
>>    JOURNAL   Biochemistry 31 (14), 3611-3617 (1992)
>>     PUBMED   1567819
>> REFERENCE   2  (bases 1 to 9)
>>    AUTHORS   Kristensen,T.
>>    TITLE     Direct Submission
>>    JOURNAL   Submitted (11-JUN-1991) T. Kristensen, Dept of
>> Mol Biology,
>>              University of Aarhus, C F Mollers Alle 130,
>> DK-8000 Aarhus C,
>>              DENMARK
>> FEATURES             Location/Qualifiers
>>       source          1..9
>>                       /organism="Bos taurus"
>>                       /mol_type="mRNA"
>>                       /db_xref="taxon:9913"
>>                       /clone="pBB2I"
>>                       /tissue_type="liver"
>>       gene            <1..>9
>>                       /gene="beta-2-gpI"
>>       CDS             <1..>9
>>                       /gene="beta-2-gpI"
>>                       /codon_start=1
>>                       /product="beta-2-glycoprotein I"
>>                       /protein_id="CAA42669.1"
>>                       /db_xref="GI:6"
>>                       /db_xref="GOA:P17690"
>>                       /db_xref="UniProtKB/Swiss-Prot:P17690"
>>
>> /translation="PALVLLLGFLCHVAIAGRTCPKPDELPFSTVVPLKRTYEPGEQI
>>
>> VFSCQPGYVSRGGIRRFTCPLTGLWPINTLKCMPRVCPFAGILENGTVRYTTFEYPNT
>>
>> ISFSCHTGFYLKGASSAKCTEEGKWSPDLPVCAPITCPPPPIPKFASLSVYKPLAGNN
>>
>> SFYGSKAVFKCLPHHAMFGNDTVTCTEHGNWTQLPECREVRCPFPSRPDNGFVNHPAN
>>
>> PVLYYKDTATFGCHETYSLDGPEEVECSKFGNWSAQPSCKASCKLSIKRATVIYEGER
>>
>> VAIQNKFKNGMLHGQKVSFFCKHKEKKCSYTEDAQCIDGTIEIPKCFKEHSSLAFWKT
>>                       DASDVKPC"
>>       sig_peptide     <1..>9
>>                       /gene="beta-2-gpI"
>> ORIGIN
>>          1 ccagcgctc
>> //
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