[Bioperl-l] Retaining seqnos from clustal output in AlignIO

[Lee Katz]

Hi, I have a large Clustal alignment but I want to sort the sequences and
retain the coordinate numbers on the sides.  I've also hacked in strand
information into the sequence name, but that's another story.

How can I use an "in" alignio and an "out" alignio and still retain the
coordinate numbers?  I can't find an option to keep them.  Thanks.

SeqYYY.fna/1/232361-241520
TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50
SeqZZZ.fna/1/233928-243087
TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50
AnotherSeq.fna/1/1-10089
TTCGGCTTAAACCTTATCCATATCCAAACGCATAACCGTAACCCATTCAC 50

-- 
Lee Katz