[Bioperl-l] simple PrimarySeq question

[Niels Larsen]

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
//