[Bioperl-l] SeqIO - masked seqs

chauser charlesh at admin.stedwards.edu
Tue Mar 15 18:44:16 EST 2005


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 



------------- EXCEPTION  -------------
MSG: Got a sequence with no letters in it cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet 
STACK Bio::Seq::SeqFastaSpeedFactory::create 
STACK Bio::SeqIO::fasta::next_seq 
STACK main::RAW ESTcleanup.pl:81
STACK toplevel ESTcleanup.pl:49

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