[Bioperl-l] How do you add a consensus to AlignIO?

[Wes Barris]

Jason Stajich wrote:

> Try:
>  my $consensus = new Bio::LocatableSeq(-seq=>$aln->consensus_string(),
>                                         -id=>'btcn1000');

Thanks.  That did the trick almost (I had to add -start and -end to the
argument list).  However, it is not producing the consensus in the way
that I want.  Here is a portion of the resulting msf file:

AU278862              ---------- ---------C TCTACAGAAT CTGTGTTTAT TTTGTTTCAG
AU278567              ---------- ---------- ---ACAGAAT CTGTGTTTAT TTTGTTTCAG
AU277959              -------AGA TTTTGACATC TCTACAGAAT CTGTGTTTAT TTTGTTTCAG
AU278008              CCTTCTTANA TTTTGACATC TCTACAGAAT CTGNGTTTAT TTTGTTTCAG
AU278623              -------AAA TTTTGACATC TCTACANAA- CTGTGTTTAT TTTGTTTCAN
AU278682              -------AAA TTTTGACATC TCTACANAAT CTGTGTTTAT TTTGTTTCAN
BM031781              ---------- ---------- ---------- ---------- ----------
consensus             -------A-A TTTTGACATC TCTACAGAAT CTGTGTTTAT TTTGTTTCAG

I need the consensus to span the entire alignment length like this:

consensus             CCTTCTTAAA TTTTGACATC TCTACAGAAT CTGTGTTTAT TTTGTTTCAG

i.e. I need it to ignore where the aligned sequences do not exist.  Is there
a way to make it do that?

-- 
Wes Barris
E-Mail: Wes.Barris at csiro.au