[Bioperl-l] RangeI.pm warnings

[Luc.Gauthier at aventis.com]

Hi everyone,

I use the SearchIO mechanism to parse BLASTN 2.1.3 reports.

I yesterday downloaded an upgrade to the bioperl-live library I currently use
for my developments.
The problem is that since then, I get the following warning messages from
RangeI.pm :

-----
Argument "start" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 505.
Argument "end" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 506.
Argument "strand" isn't numeric in i_negate at
/home/local/lgauthie/dev/perl5lib/Bio/RangeI.pm line 507.
-----

Here is how it happens...

First, I get a raw blastall report from a wrapper tool I wrote :
     my $result = $self->_run_ReadWrite($toolpath, $toolparams,
$params{query});
     my $raw_report = join "\n", @{$results->{OUTPUT}};

Then I instantiate an IO::String (v1.03) object from the obtained string :
     my $pseudoFH = IO::String->new( $raw_report );

Finally, I want to obtain a Bio::SearchIO report from that :
     my $searchIO = Bio::SearchIO->new( -format => 'blast' , -fh => $pseudoFH
);


And this is that command that brings the warnings messages from RangeI.pm.

One interesting thing is that when I parse blast reports in a loop, only the
first Bio::SearchIO
report creation will bring the warning messages...

Has anyone else seen that problem ?

Thank you for reading, and have a good day !
Luc Gauthier