[Bioperl-l] entrezgene binary ASN

[Michael Seewald]

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> 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
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-- 
Dr. Michael Seewald
Bioinformatics
Bayer HealthCare AG