bioperl/bioperl-live — pull request #27 by fgvieira (2011-11-04 19:25:09+00:00)
Title: Changed _get_len() at AlignIO::fasta.pm

Changed _get_len() at AlignIO::fasta.pm to be compatible with _ungapped_len() at LocatableSeq.pm

The different assumption of RESIDUE symbols in both modules caused, sometimes, a warning.
My specific case was with a MSA with undetermined positions (?) that were stripped in AlignIO::fasta.pm but not in LocatableSeq.pm, giving different total lengths (and a warning). Both functions should give the same length and I opted to change AlignIO::fasta.pm (although changing LocatableSeq.pm would also be acceptable).

FGV