[BioPython] Deprecating Bio.Saf (PredictProtein Simple Alignment Format)

[Peter]

Is anyone using Bio.Saf or PredictProtein's "Simple Alignment Format" (SAF)?

Bio.Saf is one of the older parsers in Biopython.  It parses the
PredictProtein "Simple Alignment Format" (SAF), a fairly free-format
multiple sequence alignment file format described here:
http://www.predictprotein.org/Dexa/optin_saf.html

Potentially we could support this file format within Bio.AlignIO (if
there was any demand).  However, as far as I can tell, this file
format is ONLY used for PredictProtein, and they will accept several
other more mainstream alignment file formats as alternatives.

Bio.Saf uses Martel for parsing, which is not entirely compatible with
mxTextTools 3.0.  If we did want to integrate SAF support into
Bio.AlignIO it might be best to reimplement the parser in plain
python.

If no one is using it, I would like to deprecate Bio.Saf in the next
release of Biopython.

Peter