[Bioperl-l] From Contig to MSA

[Lewis, Christopher]

Hello,

Apologies in advance if this has already been answered - google turned
up nothing.

Yesterday I sat down and wanted to extract the alignment from an ace
file produced by phrap.  So I used Bio::Assembly::IO to read in the ace
file.  Then I attempted to use Bio::AlignIO to write the MSA (in
clustalw or msf format).  I quickly discovered that
Bio::Assembly::Contig.pm doesn't implement many of the methods defined
in AlignIO.pm and that I can't use write_aln to write the contig.

A quick search turned up the following:
http://bioperl.org/pipermail/bioperl-l/2003-September/013309.html

However, if the suggested method to create a flushed alignment has been
created, I can't find it.  Has this been implemented?  Is this still
considered desirable?

cheers,
Chris

  

Christopher T. Lewis
Agriculture and Agri-Food Canada/Agriculture et Agroalimentaire Canada
LewisCT at agr.gc.ca