[Bioperl-l] trying to save blast hit sequences to fasta file

Alicia Amadoz Alicia.Amadoz at uv.es
Wed Aug 1 03:13:11 EDT 2007


Hi, I would like to save my hit sequences from a blast result in a fasta
file. I am trying some things but I have problems using Bio::SearchIO
and Bio::SeqIO. Hope anyone could help me with this. Here is my current
code:

# my $seq_out = Bio::SeqIO->new("-file" => ">$fasfilename", "-format" =>
"fasta");
my $seq_out = Bio::SearchIO->new("-file" => ">$fasfilename", "-format"
=> "fasta");
while(my $result = $blast_report->next_result()) {
   while(my $hit = $result->next_hit()) {
      while(my $hsp = $hit->next_hsp()) {
         my $hseq = $hsp->hit_string();
         # $seq_out->write_seq($hseq);
         $seq_out->write_result($hseq);
      }
   }
}

Here the error is,

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: ResultWriter not defined.

I couldn't find any kind of documentation about ResultWriter.
Thanks in advance,
Alicia




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