[Bioperl-l] Re: entrezgene binary ASN

[Michael Seewald]

Hi Stefan,

There are ways to capture these errors. Perl exception handling might
be way to do it.

On the other hand: Wouldn"t incomplete .gz downloads throw an error
right away? I have to check (but can't right now).

Michael

On 9/20/05, Stefan Kirov <skirov at utk.edu> wrote:
> Michael,
> What if gene2xml fails (incomplete downloads, etc.)? I would prefer to
> keep it separate, but I see some people would prefer your way. My
> intention was not to rewrite the parser- it should work fine on the
> converted ags file. Thanks for the contribution!
> Stefan
>
> Michael Seewald wrote:
>
> >
> > Hi Stefan,
> >
> > The most convenient way would be to open it as a pipe:
> >
> > my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i
> > Homo_sapiens.ags.gz -c -x -b | ");
> > while(my $result = $parser->next_seq) {
> > #...
> > }
> >
> > It may be actually faster than before, because you save disk I/O. And
> > even better, there is no need to rewrite the parsers.
> >
> > Best wishes,
> > Michael
> >
> >
> > On 9/16/05, *Stefan Kirov* <skirov at utk.edu <mailto:skirov at utk.edu>>
> > wrote:
> >
> >     NCBI provides now only the binary ASN format. Entrezgene parser
> >     will not
> >     parse it, but you can convert with gene2xml:
> >
> >     RT - Shiryayev, Sergey (NIH/NLM/NCBI) wrote:
> >
> >
> >     >>Stefan,
> >     >>
> >     >>Try this:
> >     >>
> >     >>./gene2xml -i All_Data.ags.gz -c -x -b | more
> >     >>
> >     >>
> >     >>Sergey Shiryayev
> >     >>NCBI Contractor
> >     >
> >     Note that you shoul proceed the gzipped file.
> >     Stefan
> >     _______________________________________________
> >     Bioperl-l mailing list
> >     Bioperl-l at portal.open-bio.org <mailto:Bioperl-l at portal.open-bio.org>
> >     http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >     <http://portal.open-bio.org/mailman/listinfo/bioperl-l>
> >
> >
> > --
> > Dr. Michael Seewald
> > Bioinformatics
> > Bayer HealthCare AG
>
>
> --
> Stefan Kirov, Ph.D.
> University of Tennessee/Oak Ridge National Laboratory
> 5700 bldg, PO BOX 2008 MS6164
> Oak Ridge TN 37831-6164
> USA
> tel +865 576 5120
> fax +865-576-5332
> e-mail: skirov at utk.edu
> sao at ornl.gov
>
> "And the wars go on with brainwashed pride
> For the love of God and our human rights
> And all these things are swept aside"
>
>


--
Dr. Michael Seewald
Bioinformatics
Bayer HealthCare AG