[Bioperl-l] New Blast parser

[Sendu Bala]

Back in August of last year I introduced Bio::PullParserI, a module that 
aids in the creation of fast SearchIO and Search modules. I've finally 
gotten around to implementing a Blast parser using the interface, which 
I've called Bio::SearchIO::blast_pull.

To use it you say:

my $sio = Bio::SearchIO->new(-format => "blast_pull", -file => "file");

or in the near future (when I've committed StandAloneBlast changes):

my $sab = Bio::Tools::Run::StandAloneBlast->new(-_READMETHOD => 
"blast_pull");


Currently the parser is incomplete: I've only tested it with NCBI BLASTN 
and BLASTP. However, results are promising. In one particular real-world 
usage-case involving running and parsing multiple Blast jobs via 
StandAloneBlast (amongst other things), changing only the _READMETHOD 
from 'blast' to 'blast_pull' in the code dropped run time from 20223s to 
951s (~20x faster) and memory usage from over 8GB to less than 5GB (~40% 
less).

Please try it out and feed-back any bugs you discover.


Cheers,
Sendu.