[Bioperl-l] AlignIO

[ashwoo]

Dear All,
              I have a script which parses the best HSP alignment out
of BLAST result and writes it to a temporary file.

my $aln = $hsp->get_aln;
1. my $out = Bio::AlignIO->new(-file => ">tmp.aln",
2.                                 -format => 'clustalw');
3. $out->write_aln($aln);


I randomize the alignment within the "tmp.aln" file to generate a new
file "mult_rand.aln" containing all randomized alignments in clustalw
format.
Now I want to read each alignment in the randomized file hence I use

4. my $in  = Bio::AlignIO->new(-file   => "mult_rand.aln",
5.                                           -format => 'clustalw');
6. while ( my $aln = $in->next_aln() ) {
7.   #"RUN RNAZ to check the conservedness of each randomized
alignment"
8.   #NOT GETTING ANY VALUES HERE
9.   }

But I am not able to access each alignment. When I open the randomized
aln file with a separate script and same code in lines 4-9  it works
fine. Is this happening due to my using AlignIO objects twice in the
same script. Please Help.

yours sincerely,
Perl Novice