[Bioperl-l] reading blast report

Siddhartha Basu sidd.basu at gmail.com
Thu Jan 14 14:15:04 EST 2010


Hi, 
I have a script that reads a tblastn report(13000 records) and loads in
a chado database(Bio::Chado::Schema module),  however the machine runs of memory. I am trying to figure 
out other than loading the database stuff 
if it the reading of SearchIO module could consume a lot of memory. So,
when i am reading a blast file and getting the result object ....

while (my $result = $searchio->next_result)

* Does the searchio object loads a huge chunk of file in the memory or
  for each iteration it only reads a part of the result.

* Does doing an index on blast report and then reading from it be much
  faster and why. And is there any way i could iterate through each
  record in the index,  will that be helpful.

-siddhartha




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