[Bioperl-l] Error when calling remove_gaps

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Feb 15 11:32:22 EST 2005


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:


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


Any ideas?

Thanks in advance


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