[Bioperl-l] Error parsing blast results with blasttable

[michael watson (IAH-C)]

Hi

I have looked through the archives and this problem did come up once
before, but without resolution (as far as I can see).  I'm using
bioperl-1.4 and NCBI blast with the -m option, using SearchIO and the
blasttable format.

What I see is this:

------------- EXCEPTION  -------------
MSG: Undefined sub-sequence (3264,3268). Valid range = 3252 - 3268
STACK Bio::Search::HSP::HSPI::matches
/usr/local/bioperl-1.4/Bio/Search/HSP/HSPI.pm:711
STACK (eval) /usr/local/bioperl-1.4/Bio/Search/SearchUtils.pm:365
STACK Bio::Search::SearchUtils::_adjust_contigs
/usr/local/bioperl-1.4/Bio/Search/SearchUtils.pm:364
STACK Bio::Search::SearchUtils::tile_hsps
/usr/local/bioperl-1.4/Bio/Search/SearchUtils.pm:170
STACK Bio::Search::Hit::GenericHit::start
/usr/local/bioperl-1.4/Bio/Search/Hit/GenericHit.pm:899
STACK main::parse_blast ../split_and_blast.pl:65
STACK toplevel ../split_and_blast.pl:32

--------------------------------------

The code is as you would expect:

while (my $result = $searchio->next_result) {
        while(my $hit = $result->next_hit) {
                my $start  = $hit->start;

And it is that call to $hit->start that sets off the whole trace.

Any ideas?

Thanks
Mick

Michael Watson
Head of Informatics
Institute for Animal Health,
Compton Laboratory,
Compton,
Newbury,
Berkshire RG20 7NN
UK

Phone : +44 (0)1635 578411 ext. 2535
Mobile: +44 (0)7990 827831
E-mail: michael.watson at bbsrc.ac.uk