[Bioperl-l] EST Alignment questions

[Lincoln Stein]

I want to build the alignment up a step at a time from BLAT output.  BLAT 
represents the alignment as a series of non-gapped pairs.  To represent the 
alignment correctly you have to add the appropriate pad characters.

Also I need to insert HTML so that nonaligned bases change color, and AlignIO 
doesn't have the appropriate callbacks.  But that's a minor issue.

Lincoln


On Friday 01 November 2002 10:20 am, Jamie Hatfield wrote:
> > 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.
>
> ------------------------------------------------------------------------
> -
> Jamie Hatfield                                Room 541H, Marley Building
> Systems Programmer                            University of Arizona
> Arizona Genomics Computational                Tucson, AZ  85721
>   Laboratory (AGCoL)                          (520) 626-9598
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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