[Bioperl-l] EST Alignment questions

[Jamie Hatfield]

> From: Lincoln Stein [mailto:lstein@cshl.org] 
> <snip>
> What we need is a text-based alignment pretty-printer that 
> will accept 
> SimpleAlign alignments and output them with the pads 
> inserted.  The BioPerl 
> alignment modules have been written to do the inverse task-- to parse 
> pretty-printed alignments produced by external programs.

What would be wrong with using code like

|  my $Align = new Bio::SimpleAlign();
|  my $out = Bio::AlignIO->new(-fh => \*STDOUT, -format => 'clustalw');
|  $out->write_aln($Align);

to get the alignment?  I guess the fact that it has to send output to a
file is a bummer, but other than that, would it "do"?  Or are you
wanting back one line at a time?

In a totally unrelated, newbie question, why do some objects (like
SimpleAlign) get instanciated with a new whereas others (like AlignIO)
are instanciated with a method?  Or is new Bio::SimpleAlign() the same
as Bio::SimpleAlign->new()?  (pardon my ignorance, please)

Thanks.

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Jamie Hatfield                                Room 541H, Marley Building
Systems Programmer                            University of Arizona
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