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

[Peter]

On Wed, Jul 23, 2008 at 11:12 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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.

I got in touch with PredictProtein, and Burkhard Rost told me:
>> SAF is a simplified subset of MSF, actually it is
>> MSF - checksum AND + more flexibility in terms of line length asf.

I also said he was aware of several groups who used it/adopted SAF,
but didn't have any names to hand.

> 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.

I suspect adding support for the MSF alignment format to Bio.AlignIO
would be of more general interest.

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

Still no objections?

Peter