[Bioperl-l] Mapping between aligment position and reference (1st) sequence position for MAF files

[avilella]

On Wed, 2004-04-21 at 18:22, Jason Stajich wrote:
> If I understand your question correctly...
> 
> I've added a method to Bio::Coordinate::Utils for getting the alignment
> position (column) for a specific position in the reference sequence.  It
> is called from_seq_to_alignmentpos().
> 
> If you want to get the reverse

yes, this one, although the other one is also useful:

getting into account that there is the offset in each piece of aln in
the maf file...

Thanks,

    Albert.

PD: I can't update it from the cvs, but I suppose it's the lag in the
server

>  - a reference position from the alignment
> you should just be able to do:
> my $seq = $aln->get_seq_by_pos(1);
> my $ref_loc = $se->location_from_column($column);
> 
> # see what that position is:
> print $ref_loc->to_FTstring(),"\n";
> 
> -jason
> 
> On Wed, 21 Apr 2004, avilella wrote:
> 
> > Hi,
> >
> > I was wondering which is the best way to get a mapping between the
> > alignment position of a MAF file and the reference sequence position, in
> > that case for the first individual in the file.
> >
> > I would like to be able to associate the result of an analysis for a
> > position in a MAF alignment to the reference sequence.
> >
> > If not being done before, which is the best place to implement that?
> >
> > Thanks,
> >
> >     Albert.
> >
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu