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

zoujing 1zoujing at 163.com
Thu Apr 10 05:08:52 UTC 2008

  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.

More information about the Bioperl-l mailing list