[Bioperl-l] Bio::ASN1::EntrezGene parse so slowly?

zoujing 1zoujing at 163.com
Wed Apr 16 22:55:47 EDT 2008


Thank you vey much!
  Solved the problem now.

   Jing

Sean Davis-3 wrote:
> 
> gene_info is a tab-delimited text file, if I recall correctly.  Have
> you looked at it?  If it is, you should be able to parse it in a few
> seconds with just a couple lines of code.
> 
> Sean
> 
> 
> On Thu, Apr 10, 2008 at 1:08 AM, zoujing <1zoujing at 163.com> wrote:
>>
>>   I want to parse a file "gene_info" from NCBI. The format of Gene in
>> NCBI is
>>  ASN1, right? So I used Bio::ASN1::EntrezGene. But it didn't work
>>  properly/too slow. The file is about 500M.
>>   The code is following:
>>   use Bio::ASN1::EntrezGene;
>>   my $parser = Bio::ASN1::EntrezGene->new('file' => $ARGV[0]);
>>   my $i = 0;
>>   while(my $result = $parser->next_seq)
>>   { last; #something to do there, here use last for test}
>>
>>   When it goes to the "while" part, it is processing on and on, it does
>> not
>>  went out, even I used "last" in the "while" part.
>>    So I wonder whether it is too slow or the module is not fit for this
>> job,
>>  or I did something wrong?
>>
>>   Thank you!
>>  --
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>>
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