[Bioperl-l] Question about parsing a gb file
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)
More information about the Bioperl-l