[Bioperl-l] Bio::Tools::IUPAC inconsistency

[Aaron J. Mackey]

The problem is that Bio::Tools::IUPAC doesn't know that your first 
sequence is DNA (it tries to guess, but guesses wrong).  Try setting 
-alphabet => "dna" in your Bio::Seq->new() call.

-Aaron

On Aug 18, 2004, at 11:03 AM, mql201 wrote:

> Hello
>
> I'm using the mod above.  I'm getting inconsistent output.  This fn, 
> which
> takes an ambiguous DNA
> sequence and returns an array of all the possible variants expanded 
> from IUPAC
> meta symbols:
>
> sub expandMeta {
>   my($uniqueseq);               # unique sequence object
>   my(@rAr) = ();                # return array
>   my($seqstr) = "";             # sequence attr of a sequence object
>
>   my($ure) = $_[0];           # upstream regulatory element (sequence 
> to
> check)
>
>   my($ambiseq) = new Bio::Seq (-seq => $ure, -type => 'Dna');
>   my($stream) = new Bio::Tools::IUPAC(-seq => $ambiseq);
>
>   while($uniqueseq = $stream->next_seq()) {
>     $seqstr = $uniqueseq->seq();
>     print("$ure -> |$seqstr|<br>");
>     ## process the unique Seq object.
>     #
>     @rAr = (@rAr, $seqstr);
>   }
>   return(@rAr);
> }
>
> when i feed it these two sequences, for example,
> ANTTW
> GGWAGGT
>
> the print statement in the while loop outputs this:
>
> ANTTW -> |ANTTW|
> GGWAGGT -> |GGAAGGT|
> GGWAGGT -> |GGTAGGT|
>
> the fact that both strings go through the loop means they're being 
> picked up,
> but i'd expect this
> kind of output:
>
> ANTTW -> |AATTA|
> ANTTW -> |ATTTA|
> ANTTW -> |ACTTA|
> ANTTW -> |AGTTA|
> ANTTW -> |AATTT|
> ANTTW -> |ATTTT|
> ANTTW -> |ACTTT|
> ANTTW -> |AGTTT|
> GGWAGGT -> |GGAAGGT|
> GGWAGGT -> |GGTAGGT|
>
> I suspect this is an easy one, but i can't see where its going wrong.
>
> many thanks IA
> mark
>
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>
--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697