[Bioperl-l] Parsing blast report

[gert thijs]

I have found the solution to this problem. I defined $DEBUG=1 in my script and
this triggers some action in Bio::Root::Object.pm

Gert


gert thijs wrote:
> 
> Hi,
> 
> I have a problem processing blast reports that I didn't saw before I installed
> the latest version of bioperl. To parse the blast report I use BPlite.
> I am parsing every report in a list of blast reports. The problem is that
> there is output generated on STDERR that has to be confirmed with an enter.
> This is of course annoying if you try to autmate the blast process. An example
> of the ouptu can be found below. These are only the first few lines, but there
> are much more lines in the output. It seems that there is some problem
> initializing an object, but I am not  familiar enough with the object
> structure of bioperl to detect what goes wrong.
> Has anyone any idea about this?
> 
> PROGRAM:
> foreach $r (@Reports) {
>     tie *IN, 'IO::Scalar', \$r;
>     my $blast = Bio::Tools::BPlite->new(\*IN);
>     while( (my $sbjct = $blast->nextSbjct) ){
>         #process the hit
>     }
>     close(IN);
> }
> 
> OUTPUT:
> >>>> Initializing Bio::Root::Object (Bio::Tools::BPlite) anon
> ---> Initialized Bio::Root::Object (Bio::Tools::BPlite)
> >>>> Initializing Bio::Root::Object (Bio::Tools::BPlite::Sbjct) anon
> ---> Initialized Bio::Root::Object (Bio::Tools::BPlite::Sbjct)
> >>>> Initializing Bio::Root::Object (Bio::Tools::BPlite::HSP) anon
> ---> Initialized Bio::Root::Object (Bio::Tools::BPlite::HSP)
> >>>> Initializing Bio::Root::Object (Bio::SeqFeature::Similarity) anon
> ---> Initialized Bio::Root::Object (Bio::SeqFeature::Similarity)
> ...
> 
> --
> ==========================================================
> + Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
> +                                                        +
> + Dept. Elektrotechniek ESAT-SISTA                       +
> + Kardinaal Mercierlaan, 94                              +
> + B-3001 HEVERLEE  Belgium                               +
> + Tel :  +32-16-32 18 84 ---- Fax : +32-16-32 19 70      +
> ==========================================================
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

-- 
==========================================================
+ Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
+                                                        +
+ Dept. Elektrotechniek ESAT-SISTA                       +
+ Kardinaal Mercierlaan, 94                              +
+ B-3001 HEVERLEE  Belgium                               +
+ Tel :  +32-16-32 18 84 ---- Fax : +32-16-32 19 70      +
==========================================================