[Bioperl-l] Re: entrezgene binary ASN

[Mingyi Liu]

I'll try to handle it transparently (not difficult) and make sure it 
doesn't break anything.  Anyway this is only related to 
Bio::ASN1::EntrezGene, not Bio::SeqIO::entrezgene, which should not be 
concerned about the low level I/O in our structure.

Mingyi

Michael Seewald wrote:

>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
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>>>
>>>
>>>--
>>>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
>
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