[Bioperl-l] Problems to get secondary accessions

[stephan]

Hi,

because I have still the same trouble,
here is a example to retrace my problem.

After a collection is added, the second call 
($seq->get_secondary_accessions) gives nothing back.

I get only: HAL007 C3PO01

Is it a bug, a feature, or normal behavior - ?
I am a little bit confused -
I am using bioper 1.4.

regards
stephan



--------- the script -----------------------------

#!/xprog/perl/perl-5.9.1_inst/bin/perl
use lib "perl5";

use strict;
$ENV{BIOPERL_INDEX_TYPE} = "SDBM_File";
$ENV{BIOPERL_INDEX} = ".";

use Bio::Index::Swissprot;

my $accs = qw(P09651);
my $file_name = "swiss.dat";
my $inx = Bio::Index::Swissprot->new(-filename => $file_name . ".idx",
-write_flag => 1);
$inx->id_parser(\&get_id);
$inx->make_index($file_name);


my $seq = $inx->fetch($accs);

my @sec1 = $seq->get_secondary_accessions;
print "@sec1\n";

my $col  = new Bio::Annotation::Collection;
my $sv   = new Bio::Annotation::SimpleValue(-value => 'foo' );
$col->add_Annotation( 'bar', $sv );
$seq->annotation($col);

my @sec2 = $seq->get_secondary_accessions;
print "@sec2\n";


sub get_id {
my $line = shift;
$line =~ /AC\s+([A-Z]\d+);/;
$1;
}



----------------And the flatfile (swiss.dat):-----------------

ID   128U_DROME     STANDARD;      PRT;   368 AA.
AC  P09651; HAL007; C3PO01;
DT   01-OCT-1993 (Rel. 27, Created)
DT   01-OCT-1993 (Rel. 27, Last sequence update)
DT   01-FEB-1996 (Rel. 33, Last annotation update)
DE   GTP-binding protein 128UP.
GN   128UP OR GTP-BP.
OS   Drosophila melanogaster (Fruit fly).
OC   Eukaryota; Metazoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC   Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha;
OC   Ephydroidea; Drosophilidae; Drosophila.
OX   NCBI_TaxID=7227;
RN   [1]
RP   SEQUENCE FROM N.A.
RC   STRAIN=Oregon-R;
RX   MEDLINE=94166747; PubMed=8121394;
RA   Sommer K.A., Petersen G., Bautz E.K.F.;
RT   "The gene upstream of DmRP128 codes for a novel GTP-binding protein
RT   of Drosophila melanogaster.";
RL   Mol. Gen. Genet. 242:391-398(1994).
CC   -!- SIMILARITY: Belongs to the GTP1 / OBG family.
CC 
--------------------------------------------------------------------------
CC   This SWISS-PROT entry is copyright. It is produced through a 
collaboration
CC   between  the Swiss Institute of Bioinformatics  and the  EMBL 
outstation -
CC   the European Bioinformatics Institute.  There are no  restrictions 
on  its
CC   use  by  non-profit  institutions as long  as its content  is  in 
no  way
CC   modified and this statement is not removed.  Usage  by  and for 
commercial
CC   entities requires a license agreement (See 
http://www.isb-sib.ch/announce/
CC   or send an email to license at isb-sib.ch).
CC 
--------------------------------------------------------------------------
DR   EMBL; X71866; CAA50701.1; -.
DR   PIR; S42582; S42582.
DR   FlyBase; FBgn0010339; 128up.
DR   GO; GO:0005525; F:GTP binding; IDA.
DR   InterPro; IPR006074; GTP1/OBG_dom.
DR   InterPro; IPR006073; GTP1_OBG.
DR   InterPro; IPR006169; GTP1_OBG_sub.
DR   InterPro; IPR005225; Small_GTP.
DR   InterPro; IPR004095; TGS_dom.
DR   Pfam; PF01018; GTP1_OBG; 1.
DR   Pfam; PF02824; TGS; 1.
DR   PRINTS; PR00326; GTP1OBG.
DR   TIGRFAMs; TIGR00231; small_GTP; 1.
DR   PROSITE; PS00905; GTP1_OBG; 1.
KW   GTP-binding.
FT   NP_BIND      71     78       GTP (By similarity).
FT   NP_BIND     117    121       GTP (By similarity).
FT   NP_BIND     248    251       GTP (By similarity).
SQ   SEQUENCE   368 AA;  41129 MW;  07C592292BA12A6E CRC64;
      MITILEKISA IESEMARTQK NKATSAHLGL LKANVAKLRR ELISPKGGGG GTGEAGFEVA
      KTGDARVGFV GFPSVGKSTL LSNLAGVYSE VAAYEFTTLT TVPGCIKYKG AKIQLLDLPG
      IIEGAKDGKG RGRQVIAVAR TCNLIFMVLD CLKPLGHKKL LEHELEGFGI RLNKKPPNIY
      YKRKDKGGIN LNSMVPQSEL DTDLVKTILS EYKIHNADIT LRYDATSDDL IDVIEGNRIY
      IPCIYLLNKI DQISIEELDV IYKIPHCVPI SAHHHWNFDD LLELMWEYLR LQRIYTKPKG
      QLPDYNSPVV LHNERTSIED FCNKLHRSIA KEFKYALVWG SSVKHQPQKV GIEHVLNDED
      VVQIVKKV
//