[Bioperl-l] Parse problem of a big EMBL entry

brian li brianli.cas at gmail.com
Tue Apr 28 23:14:23 EDT 2009


Hi everyone,

     Here is greeting from Brian.

     I have just began to use bioperl 1.6.0 to collect certain data
lines from EMBL files.

     There's a problem when I try to get an entry that includes over 1
million lines. A call of Bio::SeqIO::embl->next_seq would just cause
the parser script to exit. I have read Bio/SeqIO/embl.pm and I think
one possible way to solve the problem may be to give my script more
memory to store the entry data. The machine I am using has 32GB
memory, and that shall be enough for any entry.

     So I am wondering whether there is any way to set the size of the
memory available to a perl script. Others ways to deal with the
problem are also welcome.

     Appreciate your help.

Brian


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