[Bioperl-l] reading blast report

Jason Stajich jason at bioperl.org
Thu Jan 14 14:53:29 EST 2010


What aspects of the report are you loading?  You might consider the  
blast report as tab-delimited (-m 8 format) if you only are interested  
in start/end positions and scores of ailgnments which is a simpler and  
reduced dataset that has lower memory footprint by the parser.

Searchio (default) -format => blast - you can try the BLAST -format =>  
blast_pull instead which lazy parses to create objects and will reduce  
memory consumption.

-jason
On Jan 14, 2010, at 11:15 AM, Siddhartha Basu wrote:

> 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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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org
http://fungalgenomes.org/



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