[Bioperl-l] problem with Bio::SeqIo KEGG - need help urgently

neeti somaiya neetisomaiya at gmail.com
Mon Nov 19 01:11:49 EST 2007


Hi,

I am using Bio::SeqIO for parsing KEGG gene ent files.

A part of my code is

foreach my $key ( $ac->get_all_annotation_keys() )
                                {
                                        if($key eq "dblink")
                                        {
                                                my %values =
$ac->get_Annotations($key);
                                                foreach my $value (
keys(%values ))
                                                {
                                                        print "\n*****VALUE
$value*****\n";
                                                }
                                        }
                                 }

Here not all dblinks present in the actual file get parsed. For eg, in the
data below,
ENTRY       116064            CDS       H.sapiens
NAME        LRRC58
DEFINITION  leucine rich repeat containing 58
POSITION    3q13.33
MOTIF       Pfam: SdiA-regulated LRR_1
            PROSITE: LEU_RICH
DBLINKS     NCBI-GI: 153792305
            NCBI-GeneID: 116064
            HGNC: 26968
            Ensembl: ENSG00000163428
            UniProt: Q96CX6

Here, the dblink parsing gives me NCBI-GeneID, Ensembl, Pfam and PROSITE,
but doesnt give me HGNC and UniProt. For other entries it gives me other
combinations of dbs.

Can anyone help me with this. Why is this happenning? I have no clue.

Thanks and Regards,
Neeti.
-- 
-Neeti
Even my blood says, B positive


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