[Bioperl-l] Blast Parser Error

[Lakshmi K Matukumalli]

Jason Stajich wrote:
> 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 
> <mailto: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 <mailto:jason at bioperl.org>
> http://www.duke.edu/~jes12/ <http://www.duke.edu/%7Ejes12/>

Hi Jason,

Thank you for forwarding the email. I apologize for sending the large 
attachment.

I have placed the blast file here.

http://mysite.verizon.net/lmatukum/blast/unmasked.blast

You can right click and save the blast file.

Thank you,

Lakshmi Kumar