[Bioperl-l] reading blast report
sidd.basu at gmail.com
Thu Jan 14 14:15:04 EST 2010
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.
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