[Bioperl-l] Error when calling remove_gaps

[michael watson (IAH-C)]

Hi

I'm using bioperl-1.4 on Linux.  I get the following error after calling
remove_gaps on an alignment I have read in using AlignIO.  The alignment
is in fasta format, and some sequences contain "N"'s and "-"'s as gap
characters, but some sequences do not include any, including the first
sequence.  This problem occurs when I call:

$al->remove_gaps("-")

------------- EXCEPTION  -------------
MSG: Got a sequence with no letters in - cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet
/usr/local/bioperl-1.4/Bio/PrimarySeq.pm:839
STACK Bio::PrimarySeq::seq /usr/local/bioperl-1.4/Bio/PrimarySeq.pm:280
STACK Bio::SimpleAlign::_remove_col
/usr/local/bioperl-1.4/Bio/SimpleAlign.pm:959
STACK Bio::SimpleAlign::remove_gaps
/usr/local/bioperl-1.4/Bio/SimpleAlign.pm:922
STACK toplevel create_blastable.pl:14

--------------------------------------

Any ideas?

Thanks in advance

Mick