[Bioperl-l] Blast Parser Error

Jason Stajich jason at bioperl.org
Tue Sep 19 12:13:54 EDT 2006


Forwarding your question to the bioperl mailing list where it can be
answered.  Please consider making your BLAST file available one a website -
it is bad form to mail someone a very large email attachment unsolicited.
If you do not have access to a website where you can make the report
avaialble you can submit this a bug at http://bugzilla.open-bio.org and
attached a report to the bug.

it is possible the PARACEL BLAST format is not parseable with latest code -
please let the list know what version of bioperl you are using etc.  Please
test your question against the latest code in CVS as well before you ask
others to debug this problem.

-jason

On 9/19/06, Lakshmi K Matukumalli <lmatukum at gmu.edu> wrote:
>
> Hi Jason,
>
> I am unable to get correct results with the following blast file.
> My input sequence has a repeat element so it has a number of hits.
>
> But there is only one hit with complete identity across the length of
> query.
>
> The Bioperl parser is not giving me the correct result for the first hit
> and first hsp.
>
> Can you please look into this and let me know if I am doing something
> wrong or
> if you have to fix the script.
>
> I am attaching the input file I used along with the script I used to
> print out the top hit.
>
> Thank you,
>
> Lakshmi Kumar
>
>
>
>
> use strict;
> use Bio::SearchIO;
>
> my $searchio = Bio::SearchIO->new(-file => 'unmasked.blast',
>                                   -format => 'blast');
>
> while ( my $result = $searchio->next_result() ) {
>   my $query_name = $result->query_name;
>   my ($str);
>   while( my $hit = $result->next_hit ) {
>     # process the Bio::Search::Hit::HitI object
>     while( my $hsp = $hit->next_hsp ) {
>       # process the Bio::Search::HSP::HSPI object
>       my ($qs,$qe,$hs,$he) =
> ($hsp->query->start,$hsp->query->end,$hsp->subject->start,$hsp->subject->end);
>       my ($chr,$Bts,$Bte) = ($hit->description =~ /Bos taurus chromosome
> (.*)-FRAG\[(\d+)\,(\d+)\]/);
>       $str = $query_name."\t".$chr."\t".($Bts+$hs)."\t".($Bts+$he);
>       last;
>     }
>     last;
>   }
>   print $str,"\n";
> }
>
>
>
> BLASTN 1.5.4-Paracel [2003-06-05]
>
> [SNIP]


-- 
Jason Stajich
jason at bioperl.org
http://www.duke.edu/~jes12/


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