[Bioperl-l] Simple question on reading a .msf file

Terry Jones tc.jones at jones.tc
Sun Dec 5 15:45:29 EST 2004

>>>>> "Brian" == Brian Osborne <brian_osborne at cognia.com> writes:
Brian> Try map_chars() rather than gap_chars, see if that works. It's
Brian> described in the Bio::AlignIO::msf POD.

It's not in my perldoc Bio::AlignIO::msf. It is in Bio::SimpleAlign
though.  But I tried this originally, and I can call map_chars but
then the code breaks because Bio::SimpleAlign has no next_aln().

I got another suggestion, from Stefan Kirov, to try the same thing
(map_chars). He also suggested replacing '~' with '-' outside bioperl,
and this does work. I'd like to avoid it though, because I'd
rather not touch the .msf files outside of bioperl.

Thanks a lot,

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