[Bioperl-l] about the iupac

[Brian Osborne]

Magic,

The code works. The documentation is old, you should say "-alphabet => dna",
not "-type".

Check out the documentation in Seq.pm, to master Bioperl you must master the
Seq object.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at bioperl.org [mailto:bioperl-l-bounces at bioperl.org]On
Behalf Of Magic Fang
Sent: Wednesday, March 05, 2003 8:10 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] about the iupac

why my iupac module can not translate seq with ambigious base to the
unambigious? the codes are:
#!/usr/bin/perl
use Bio::Seq;
use Bio::Tools::IUPAC;
my $ambiseq = new Bio::Seq (-seq => 'AYTCGUTGR', -type => 'Dna');
my $stream  = new Bio::Tools::IUPAC(-seq => $ambiseq);
print $ambiseq->seq(), "\n";
while ($uniqueseq = $stream->next_seq()) {
# process the unique Seq object.
        print $uniqueseq->seq, "\n";
}

the out put are the same seq.
does this module will translate the seq to unambigious seq? doubt:-)

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