[Bioperl-l] Arrays of BioSeq and TCoffee

[James Wasmuth]

Hi people,

I have a number of fasta format sequences in one string, which I wish to 
align using T-Coffee, without writing the sequences to a file first.

According to doc for T-Coffee module, the align method will take a 
filename or an array of references for Bio::Seq objects...

I've tried the following script but it fails, I am informed that the 
first Bio::Seq object contains less than 2 sequences.  Well of course it 
does, its a Bio::Seq object...  Can anyone see my error...

my @fasta_seq = qw/  >seq1\nFTTATT  >seq2\nFTTGTT  >seq3\nFTATTT /;
my @seq;
foreach (@fasta_seq)    {
        my $stringfh = new IO::String($_);
        my $seqio = new Bio::SeqIO(-fh => $stringfh, -format => 'fasta');
        push @seq ($seqio_obj->next_seq);  
    }
# here I know that @seq is an array of Bio::Seq objects

my @params = (some params);
my $factory = new Bio::Tools::Run::Alignment::TCoffee (@params);
my $aln = $factory->align(@seq);


Can a Bio::Seq object hold more than one sequence? Is that my problem

Many Thanks

J