From looking at the source, I think this is equivalent:

use Bio::LocatableSeq ();
use Bio::SimpleAlign  ();
    
my $aln = Bio::SimpleAlign->new();

foreach (qw/ AAAAAAAAAAAAAAA AAAAAAAGGAAACCA /) {
   $aln->add_seq(
      Bio::LocatableSeq->new(
         '-seq'   => $_,
         '-start' => 1,
         '-end'   => length($_),
      )
   );
}

print("IDENTITY : ", $aln->percentage_identity, "\n");
print("CONSENSUS: ", $aln->consensus_string(28), "\n");
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You can optionally add
'-display_id'  => 'Seq'.++$seq_id,
as an argument to the Bio::LocatableSeq constructor.

Warning: This is untested code written using unfamiliar modules.

use IO::Scalar;
my $data = <<EOF;
AAAAAAAAAAAAAAA
AAAAAAAGGAAACCA
EOF
my $SH = new IO::Scalar \$data;
my $in  = Bio::AlignIO->new(-fh => $SH, -format => 'fasta');
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The requirements were to start with an array. I suppose you could create $data by joining the contents of the array, but I don't think that's enough because what I said to holli applies to you too.

Ah. y, i was concentrating more on the variable to filehandle issue rather than the actual data format.. Could still join it, though--just need an extra step to the join.. something like:

my @data = qw/AAAAAAAAAAAAAAA AAAAAAAGGAAACCA/;
my $ct = 0;
my $data = join '', map { sprintf ">Seq%d\n%s\n", ++$ct, $_ } @data;
my $SH = new IO::Scalar \$data;
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package Tie::Handle::FromArray;

use strict;
use warnings;

sub new 
{
    my $pkg = shift;
    my $handle = \do {local *HANDLE};
    
    tie *{$handle}, $pkg, @_; 
    
    return $handle;
}



sub TIEHANDLE($;$) 
{
    my $pkg = shift;
    my $ref = shift || [];

    bless( $ref, $pkg );
}

sub READLINE 
{
    return shift @{+shift}
}

"this is a false statement.";
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my $fh = Tie::Handle::FromArray->new( ["AAAAAAAAAAAAAAA", "AAAAAAAGGAA
+ACCA"] );
my $in  = Bio::AlignIO->new(-fh => $fh, -format => 'fasta');
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Your tied class doesn't add ">Seq1", ">Seq2", etc to the stream. From what I saw, leaving those out causes the whole array to be treated as a single sequence (namely "AAAAAAAAAAAAAAAAAAAAAAGGAAACCA").

I must admit I don't get what you're saying.


use strict;
use warnings;

use Tie::Handle::FromArray;

my $fh = new Tie::Handle::FromArray ( ["a","b"] );

while (<$fh>)
{
    print "$_*";
}
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prints

a*b*
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just as i would expect. can you clarify?


holli, /regexed monk/