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

[Jason Stajich]

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 - 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