Bio::ASN1::EntrezGene parse so slowly?

[zoujing]

  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!

[Sean Davis-3]

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@...> 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!
>  --
>  View this message in context: http://www.nabble.com/Bio%3A%3AASN1%3A%3AEntrezGene-parse-so-slowly--tp16602210p16602210.html
>  Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
>  _______________________________________________
>  Bioperl-l mailing list
>  Bioperl-l@...
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[zoujing]

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 <[e-mail]> 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!
>  --
>  View this message in context: http://www.nabble.com/Bio%3A%3AASN1%3A%3AEntrezGene-parse-so-slowly--tp16602210p16602210.html
>  Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
>  _______________________________________________
>  Bioperl-l mailing list
>  [e-mail]
>  http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
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