[Bioperl-l] How to rename sequences in an alignment and write_aln them

[Albert Vilella]

Hi all,

What is the preferred way to rename the sequence names for a given
alignment object (Bio::SimpleAlign) so that then one can print out
(Bio::AlignIO::write_aln) the alignment with the renamed sequences?

I found out that is a bit complicated to do it right now: the only way
I managed to do it is to mess with each Bio::LocatableSeq sequence
object, and adding back the sequences to the alignment.

Maybe we could change the half a dozen write_aln methods so that one
can directly get/set the display_names for each sequence, editing the
$aln instance, instead of going into the LocatableSeq goriness.

Comments?

Cheers,

    Albert.