[Biopython] Deprecating Bio.Clustalw?

[Peter]

Dear all,

In our most recent release, Biopython 1.52, Bio.Clustalw was
declared obsolete. This is just a label to indicate that it will at
some point be deprecated (issue a warning when used) and
later it will be removed completely.

The module provides two features - parsing Clustal alignments,
and calling the clustalw command line tool.

Bio.AlignIO took over the role for parsing alignments a year
and a half ago with Biopython 1.46 (June 2008).

More recently, Bio.Align.Applications took over the role for calling
ClustalW in Biopython 1.51 (August 17, 2009) as part of an on
going standardisation of our command line wrappers using the
built in Python module subprocess.

I recognise that Bio.Clustalw has been been widely used, and
there are likely to be many existing scripts out there using it.
Does leaving this module as "obsolete" for Biopython 1.53,
and deprecating it in Biopython 1.54 sound like a good plan?

If anyone is using it heavily, please say so - especially if you
try and update your code to use Bio.AlignIO or subprocess
and Bio.Align.Applications.

Peter