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

Brian Osborne brian_osborne at cognia.com
Sun Dec 5 16:55:26 EST 2004


I'm puzzled about something. I'm looking at msf.pm and it looks like it
_should_ work, even with the tilde's in there. Can you send me the file?


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Terry Jones
Sent: Sunday, December 05, 2004 3:45 PM
To: Brian Osborne
Cc: bioperl-l at bioperl.org
Subject: RE: [Bioperl-l] Simple question on reading a .msf file

>>>>> "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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