[Bioperl-l] parsing output from an avid alignment

[Jonathan Manning]

Thanks for the reply,

Actually, I solved it by writing a short script to parse the avid output
into fasta format, which I then parsed via AlignIO and passed to the
Vista wrapper.

Cheers,

Jon

On Tue, 2004-06-08 at 16:51, Shawn Hoon wrote:
> Using bioperl-run
> you could try using mlagan Bio::Tools::Run::Alignment::Lagan
> for alignment as well. There are wrappers for it that generate 
> SimpleAlign objects.
> Then you could use Bio::Tools::Run::Vista
> which takes in a SimpleAlign object and generates the vista plots.
> 
> The Vista wrapper actually converts the align object into a binary form 
> of the AVID output
> which makes Vista run faster.
> 
> shawn
> 
> On Jun 8, 2004, at 3:39 AM, Jonathan Manning wrote:
> 
> > Hi all,
> >
> > I'm preparing to incorporate Vista analysis into my script, and am
> > attempting to use the AVID global alignment algorithm, since they seem
> > to be associated, and likely to work well together.
> >
> > I don't think there is, but just in case I've missed something, has
> > anyone written a module to parse the AVID output? Apparently it's a
> > hybrid of the fasta and ClustalW styles. Here's an excerpt of the kind
> > of thing I mean:
> >
> > 1419  t   |
> > 1420  c   |
> > 1421  a   |
> > 1422  a   |
> > 1423  t   |
> > 1424  a   |
> > 1425  g   |
> > 1426  g   |
> > 1427  t   |
> > 1428  g - g  9
> > 1429  a - a  10
> > 1430  c - c  11
> > 1431  t - t  12
> > 1432  a   g  13
> > 1433  a - a  14
> > 1434  a - a  15
> > 1435  a   g  16
> > 1436  g - g  17
> > 1437  t   |
> > 1438  c   |
> > 1439  t   |
> > 1440  c   |
> > 1441  t   |
> > 1442  a   |
> > 1443  a   |
> > 1444  a   |
> > 1445  g   |
> >
> > Cheers,
> >
> > Jon
> >
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>