[Bioperl-l] entrezgene binary ASN

Stefan Kirov skirov at utk.edu
Tue Sep 20 08:55:10 EDT 2005


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"



More information about the Bioperl-l mailing list