[Bioperl-l] SeqIO - masked seqs

[Marc Logghe]

> All,
> 
> I ran into a glitch when reading sets of EST reads where some 
> reads are masked in their entirety - i.e. all bases are X's.
> Is there a way to either modify the alphabet to accept X or 
> some other solution?

I was not able to trace the actual fix. But there was a thread in
december/january about that.
In one of the last messages Nathan was about the fix this:
http://bioperl.org/pipermail/bioperl-l/2005-January/017829.html

Brian added a comment on this alphabet() issue.
http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SeqI
O.pm?cvsroot=bioperl
Have you tried bioperl release 1.5.0 or bioperl-release-1-5-0-rc2 ?
Guess it should be fixed there.
Is bioperl-release-1-5-0-rc2 behaving better than 1.5.0 related to the
Bio::SeqFeatureI architecture ?
Marc