[Bioperl-l] GenBank -> ACeDB

[Hilmar Lapp]

Eric Snyder wrote:
> 
> Howdy Folks,
> 
> I am looking for a new GenBank to ACEDB file converter.  I am currently using 
> something written by Martin Ferguson in 1995 but it has not evolved with the 
> Sanger chromosome-specific database models that I am using and it is generally 
> showing it age.  I would think that using the Bio::DB::GenBank module I could 
> probably write a cleaner version.  

You only want to use the DB::GenBank module if you are going to
download these sequences from NCBI (or another GenBank server).
Otherwise just use -format => 'genbank' when opening a Bio::SeqIO
stream. There is also ace.pm for supporting ACE format, so in
theoretically you should be done with the famous 3-liner

my $seqin = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
my $seqout = Bio::SeqIO->new(-fh => \*STDOUT, -format => 'ace');
while(my $seq = $seqin->next_seq()) { $seqout->write_seq($seq); }

However, the POD of Bio::SeqIO::ace.pm says that ace.pm would only
handle the sequence, not attached annotation. So, if you want
that, too, there is probably some hacking necessary ... I've
included James Gilbert (the author of ace.pm) on cc, maybe he can
clarify better.

	Hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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