[Bioperl-l] Re: [Bioperl-guts-l] BioPerl 1.5 fasta.pm->next_seq() fails on sequence

Jason Stajich jason.stajich at duke.edu
Mon Sep 12 21:01:48 EDT 2005

If you pass in the -alphabet option to Bio::SeqIO you can prevent the  
sequence object from needing to guess its alphabet.

See the Bio::SeqIO perldoc:


Sets the alphabet ('dna', 'rna', or 'protein'). When the alphabet is
set then Bioperl will not attempt to guess what the alphabet is. This
may be important because Bioperl does not always guess correctly.


On Sep 12, 2005, at 11:20 AM, John Damask wrote:

> hi
> This record appears in NCBInr:
>> gi|999554|pdb|1EFG|C Chain C, Elongation Factor G Complexed With  
>> Guanosine
> 5'-Diphosphate
>  BioPerl 1.5 throws "MSG: Got a sequence with no letters in it  
> cannot guess
> alphabet []"
>  This seems to be because the PrimarySeq->_guess_alphabet() method now
> contains a regex to remove "X" (compared with BioPerl 1.4).
> I don't want to throw away this record (or others of its type if they
> exist).
>  Suggestions on how to handle this?
>  Thanks
> John
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Jason Stajich
Duke University

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