I am not sure if i got it right but I believe the error is because Blastall expects a Bio::SeqIO object. To convert sequences to a Bio::SeqIO object which you can directly pass on to your blastall call, you may use IO::String (see bioperl documentation on SeqIO)

The following worked for me. First define a string variable to store sequences in fasta format my $sequence_string = "";
Then replace these lines in your code
push(@translated_seqs, $temp_seq) unless($temp_seq->seq() =~ /\*+/);
with
$sequence_string = $sequence_string.">".$temp_seq->display_id."\n".$temp_seq->seq."\n" unless($temp_seq->seq =~ /\*+/);
(As biohisham suggested Re^3: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object, there may be better ways to select open reading frames.)

Before calling Blast, convert the string to SeqIO object as follows:
    my $stringfh = new IO::String($sequence_string);
    my $seqio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta');

    my $blaster = Bio::Tools::Run::StandAloneBlast->new(@params);

[download]
Loop through sequences to blast and continue with whatever you want to do with your blast report
while( my $seq = $seqio->next_seq ) {
  my $blast_report = $blaster->blastall($seq);
  ...
  while( my $BLAST_result = $blast_report->next_result ) {
    ...
    while( my $hit = $BLAST_result->next_hit ) {
    ... 
    }
  }
}

[download]
The parser worked fine with the blast report in default format but failed to read the ‘blasttable’ format. I haven't understand the reason for this.

In reply to Re: BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by arun_kom
in thread BioPerl StandAloneBlast is returning unexpected undefined SearchIO object by WonkoTheSane

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