[Bioperl-l] funny GI bug

[Elia Stupka]

I am looking into this bug as we speak, but just to give a heads up to
others. Parsing genbank and printing out the primary_id (i.e. the GI
number) gives a Bio::Seq::RichSeq *object* instead of the actual GI
numbers on some records (e.g. genbank P34745  GI:1174398)

Code stripped to the bare minimum is just the standard:

use Bio::SeqIO;
my $file = shift(@ARGV);
my $seqio = Bio::SeqIO->new(-file=>"$file", -format=>"Genbank");
while (my $rec = $seqio->next_seq()) {
 my $gi = $rec->primary_id;
 print "$gi\n";
}

Looking into it now...

Elia

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