[Bioperl-l] cloning, upgrading, downgrading and conversion functionality

[Marc Logghe]

Hi,
As promised I added a number of methods to Bio::PrimarySeq, Bio::Seq and
Bio::RichSeq to enable cloning, upgrading, downgrading and conversion
functionality.
Two extra methods are available for sequence objects (directly or via the
parents):
copy() and convert_to()
This little script should show the possibilities:
#!/usr/bin/perl -w

use Bio::SeqIO;
use Bio::Seq;

use Data::Dumper;

$io = Bio::SeqIO->new(-format => 'genbank');

# Get a Bio::Seq::RichSeq object
$seq1 = $io->next_seq;

# Convert a Bio::Seq::RichSeq to a Bio::PrimarySeq object
$seq2 = $seq1->convert_to('Bio::PrimarySeq');

# Clone the Bio::PrimarySeq object
$seq3 = $seq2->copy;

# Convert Bio::PrimarySeq to Bio::Seq object
$seq4 = Bio::Seq->copy($seq3);

# Let's have a look at the objects
for ('seq1', 'seq2', 'seq3', 'seq4')
{
  print "${$_}\n",
         Data::Dumper->Dump( [${$_}],[$_] );
} <<Bio.seq.tar.gz>> 

Tried to add the pod and added a test to Seq.t. Hopefully it passes the
quality control ;-)
Regards,
Marc
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