[Bioperl-l] simple PrimarySeq question

[Kevin Brown]

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
> //
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>