[Bioperl-l] New Blast parser

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Fri May 18 08:13:38 UTC 2007


> 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.
> my $sio = Bio::SearchIO->new(-format => "blast_pull", -file => "file");
> Please try it out and feed-back any bugs you discover.

This is very cool!
Here's hoping NCBI don't change the default output format too much.

You should be able to add "rpsblast -p T" support as this is identical
to "blastall -p blastp" except for first line:
BLASTP 2.2.16 [Mar-25-2007]
RPS-BLAST 2.2.16 [Mar-25-2007]

The only problem is the (rarely used) "rpsblast -p F" mode which
looks/behaves like a "blastall -p tblastn", ie. has hit summaries with

 Score = 29.6 bits (65), Expect = 0.26
 Identities = 10/26 (38%), Positives = 12/26 (46%)
 Frame = -1

BUT has the same header line, so you can't know -p F was used until
you see a "Frame = ??" in a hit (what were they thinking???).

TBLASTN 2.2.16 [Mar-25-2007]
RPS-BLAST 2.2.16 [Mar-25-2007]    # should be RPS-TBLASTN perhaps...

Thanks for the good work. Shame I converted most of our systems to blastxml :-(


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