[Bioperl-l] help needed, please

[simabba at tin.it]

Hello!

I'm learning Perl language so I have a lot of problems, so please be patient!


Some months ago I wrote a simple Perl script for submitting sequences to
blast. This script also uses  Bio::DB::GenPept to retrieve Sequence objects.
This part of the code is: 

$gb = new Bio::DB::GenPept;
$seq = $gb->get_Seq_by_id($hn);

where $hn is the ID of the best match given by blast 

The next step is to retrieve the species to whom the sequence belongs and
its classification as Metazoa or Fungi or something else so I wrote:
$species = Bio::Species->new(-classification => [@classification]);
$species=$seq->species() if (ref $seq);
@classification=$species->classification() if (ref $seq);
$species->classification(@classification);
$bi = $species->binomial(); $cl = join ' ', @classification;
$cl=$1 if($cl =~ /(Metazoa|Viridiplantae|Fungi|Bacteria|Archaea|Eukaryota|Virus)/);

@info_spe = ($bi, $cl);
return "@info_spe";
.....


Thr problem is that this script worked until one month ago but now for every
analyzed sequence the script always returns the wrong species but the correct
classification of the species. I mean, if the putative function of my sequence
according to blast is
"hypothetical protein [Neurospora crassa]", the script returns  for example
"Mus musculus" as species (clearly a mistake!) and "Metazoa" as classification
(this is OK).
 
I tried to type the ID of the sequence in the code, in this way:

$seq = $gb->get_Seq_by_id('ref|XP_330538.1|');

but the results is the same: the wrong species.

The strange thing is that the script works correctly until one month ago.
Has something changed in GenPept???

Thank you for the help

Best regards

Simona