[Biopython-dev] Dump file in Bio/Saf/__init__.py

[Peter]

>> While we're on the subject: the functionality currently in Bio.Saf probably belongs in Bio.AlignIO.
>
> Yes, it probably does - assuming anyone still uses the file format.
> I'll take a look at that at some point.

I've been looking at the PredictProtein site's SAF (Simple Alignment
Format) specification, which as far as I know is the only definition
(spelling errors and all).  Its a free-format somewhat like PHYLIP,
and for "nice" input files parsing shouldn't be too difficult.
However, some of the corner cases they give are frankly evil, and I
wonder if Bio.Saf is actually compliant.

See http://www.predictprotein.org/Dexa/optin_safDes.html

I'd like to propose deprecating Bio.Saf on the main mailing list.

If there are people wanting to use this SAF format, we can then
worrying about implementing a non-Martel parser for this file format
in Bio.AlignIO instead - and explicitly test it can cope with all the
examples given.

Peter

P.S. I updated Bio.Saf to use the new URL for the PredictProtein site.