[Bioperl-l] convert fasta output to blast -m8?

[Amir Karger]

Hi.

I've been asked to translate Fasta output to Blast -m8 output. I could do it
by hand, but I have a feeling SearchIO & Writer can do this pretty easily.
Can someone give me a couple hints? 

I tried running a ridiculously simple script on fasta -m9 output:

use Bio::SearchIO;
my $searchio = new Bio::SearchIO(-format => 'fasta',
                                -file   => 'short.out');
while( my $result = $searchio->next_result ) {
    print $result->query_name;
}

And I got:

Use of uninitialized value in concatenation (.) or string at
/usr/local/lib/perl5/site_perl/5.8.4/Bio/Search/HSP/GenericHSP.pm line 231,
<GEN1> line 61.

------------- EXCEPTION  -------------
MSG: Did not specify a Query End or Query Begin -verbose 0 -algorithm FASTP
-score 186.3 -hit_frame 0 -hsp_length 300 -hit_seq
PPPPPPTAETFDSDQTSSFSDINSTTASAPTTPAPALPPASPEVRKEETHPKHSLPPLPNQFAPLPDPPQHNSPPQ
NNAPSQPQSNPFPFPIPEIPSTQSATNPFPFPVPQQQ--FNQAPSMGIPQQNRPLPQLPNRNNRPVPPPPPMRTTT
EGSGVRL---PAPPPP---PRRGPAPPPPPHRHVTSNTL------NSAGGNSLLPQATGRRGPAPPPPPRASRPTP
NVTMQQNPQQYNNSNRPFGYQTNSNMSSPPPPPVTTFNTLTPQMTAATGQPAVPLPQNTQAPSQATNVPVAP
-hit_length 300 -query_length 300 -query_frame 0 -swscore 212 -rank 1
-query_seq
MYQSMTVP-PFRPYGGDDIRVVSDLSRFDYQPDQKIRSRNPTPP---STINDNVSSSKLTLDTIIPLY---SSKID
ERPKYSPLRQQEDRSTQYPSPPIPVKEEPTITIPKREKKKVRYSIGVQVPQDNGGISMTNNPAPPAPVPVPVPAPA
PPPPPPKDIAPRSMPYPQDINNANNLPPMPQPTSQLYPQQQLPPLPYKDSSSITSPQKRLEKKLIKQVMNRPVIQF
KADRFGQNYEGEYFTISANFVIYVFEVCCSVVEIVLSSILLQRDQDI -homology_seq
:.: :  : .. ..:      . .  :  .  .  : ::   :  ..:. :.  .    .:.    :..    :
:. ::.   .: ::  :: ...:   .:.:... :     ...  ...:. .   :::: :   :  .:::::::
. ..  ..      :.:..   .:: :..  :    ::   . . ..:  :
-hit_name lcl|cerevisiae|YOR181W| -bits 44.0 -query_name
lcl|albicans|CA0100| -evalue 8.3e-05 (qs='
STACK Bio::Search::HSP::GenericHSP::new
/usr/local/lib/perl5/site_perl/5.8.4/Bio/Search/HSP/GenericHSP.pm:231
STACK Bio::Search::HSP::FastaHSP::new
/usr/local/lib/perl5/site_perl/5.8.4/Bio/Search/HSP/FastaHSP.pm:97
STACK Bio::Factory::ObjectFactory::create_object
/usr/local/lib/perl5/site_perl/5.8.4/Bio/Factory/ObjectFactory.pm:150
STACK Bio::SearchIO::SearchResultEventBuilder::end_hsp
/usr/local/lib/perl5/site_perl/5.8.4/Bio/SearchIO/SearchResultEventBuilder.p
m:275
STACK Bio::SearchIO::fasta::end_element
/usr/local/lib/perl5/site_perl/5.8.4/Bio/SearchIO/fasta.pm:872
STACK Bio::SearchIO::fasta::next_result
/usr/local/lib/perl5/site_perl/5.8.4/Bio/SearchIO/fasta.pm:403
STACK toplevel a.pl:8

--------------------------------------
lcl|albicans|CA0099|

(The last thing is actually the query, so it's sort of doing the right
thing. And line 61 of short.out (where the uninitialized value happens) is
the beginning of the second hit.

Running bp_filter_search.pl -format fasta -score 150 on the same output file
produced no output at all. Is -m9 confusing it? Or is there some other
problem?

Pointers to docs etc. appreciated.

-Amir Karger