[Bioperl-l] Feature Request: add -alphabet to AlignIO arguments

Chris Fields cjfields at uiuc.edu
Wed Aug 30 12:00:24 EDT 2006


We can add this in so that it is set for all AlignIO modules, but each
AlignIO 'plugin' will have to enforce it (i.e. make an explicit accession
for the alphabet type and set it appropriately).

Generally, any code enhancements are added to Bugzilla, but we accept them
here as well.  The advantage with Bugzilla is that it's easier to keep track
of these requests there.  We also accept code patches (makes it much easier
to get the changes you want, hint hint nudge nudge).

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Dexter Riley
> Sent: Tuesday, August 29, 2006 5:11 PM
> To: Bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Feature Request: add -alphabet to AlignIO arguments
> 
> 
> Hello.  Currently, when you create a new Alignment using Bio::AlignIO-
> >new(),
> the method guesses the alphabet for each sequence using its base content.
> This means that sequences with a high percentage of degeneracies may be
> misclassified as having a protein alphabet, resulting in an alignment
> object
> with some 'dna' and some 'protein' sequences.  It is possible to manually
> set the alphabet type on each sequence in the alignment, but it would be
> simpler to add an -alphabet argument to the constructor, like so:
>   my $in = Bio::AlignIO->new(
>     -file => $filename,
>     -alphabet => 'dna',
>     -format => 'clustalw');
> If the -alphabet argument is not present, the constructor would guess the
> alphabet type as before; if it is present, then that alphabet type would
> be
> applied to each sequence in the alignment.
> I'm not sure if this is the place for feature requests; if not, just let
> me
> know and i'll post over there.  Also, I apologize if this got submitted
> twice; I wasn't registered the first time.
> Thanks,
> Ed Beaty
> 
> --
> View this message in context: http://www.nabble.com/Feature-Request%3A-
> add--alphabet-to-AlignIO-arguments-tf2186532.html#a6048738
> Sent from the Perl - Bioperl-L forum at Nabble.com.
> 
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