[Bioperl-l] Question about parsing a gb file

Paolo Pavan paolo.pavan at gmail.com
Fri Mar 27 09:09:32 EDT 2009

Hi everybody,I have a little problem/question in parsing a genbank file.
I've got a $s = Bio::Seq object to which I've added
some Bio::SeqFeature::Generic, everything here seem to be ok since I can
find all the properties of the $s setted correctly in my visual debugger;
for instance, I can find the display_name properties of the SeqFeature in
the $s object.
Than I perform a print Bio::SeqIO->new(-format => 'genbank')->write_seq($s)
to write down the genbank file but there I can't get any more some
properties of the sequence, like the "display_name".
What does it happens?

Below a snip of code, thank you in advance,

my $s = $str->next_seq();

my $f = Bio::SeqFeature::Generic->new(
            -start        => 10,
            -end          => 100,
            -strand       => -1,
            -primary      => 'CDS', # -primary_tag is a synonym
            -source_tag   => 'repeatmasker',
            -display_name => 'alu family'


print Bio::SeqIO->new(-format => 'genbank')->write_seq($s)

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