[Biopython] Deprecating Bio.Fasta?

[Peter]

Hi all,

I'd like to finally deprecate the Bio.Fasta module.

Bio.SeqIO was introduced back in Biopython 1.43 (March 2007), and
in the last two years has effectively replaced Bio.Fasta as the primary
interface for reading and writing FASTA files in Biopython.

The NEWS file entry for Biopython 1.48 (September 2008) said:
> Bio.Fasta is now considered to be obsolete, please use Bio.SeqIO
> instead. We do intend to deprecate this module eventually, however,
> for several years this was the primary FASTA parsing module in
> Biopython and is likely to be in use in many existing scripts.

The Bio.Fasta docstring also clearly states the module is obsolete.
I'd like to officially deprecate Bio.Fasta for the next release (Biopython
1.51), which means you can continue to use it for a couple more
releases, but at import time you will see a warning message. See also:
http://biopython.org/wiki/Deprecation_policy

Would this cause anyone any problems? If you are still using Bio.Fasta,
it would be interesting to know if this is just some old code that hasn't
been updated, or if there is some stronger reason for still using it.

Thanks,

Peter

Note that the indexing parts of Bio.Fasta recently discussed on this
mailing list (which used Martel/Mindy and broke with mxTextTools
3.0) were explicitly deprecated Biopython 1.44 and have since been
removed. See:
http://lists.open-bio.org/pipermail/biopython/2009-June/005252.html