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

John Damask jbdamask at gmail.com
Mon Sep 12 11:28:04 EDT 2005


hi
This record appears in NCBInr:
>gi|999554|pdb|1EFG|C Chain C, Elongation Factor G Complexed With Guanosine 
5'-Diphosphate
XXXXXXXXXXXXXXXXXXXXXXXXXXXX
 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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