[Bioperl-l] Problems to get secondary accessions

[Brian Osborne]

Stephan,

Please test using Bioperl 1.5.1.

Brian O.


On 11/13/05 2:12 PM, "stephan" <stephan.rosecker at ish.de> wrote:

> 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
> //
> 
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