[Biopython-dev] Cleaning up Bio.SeqUtils

[Peter]

On Fri, Sep 26, 2008 at 10:54 AM, Thomas Sicheritz-Ponten
<thomas at cbs.dtu.dk> wrote:
> Ok, fair enough :-)
> Please remove also the OBSOLETE tag - as Bio.SeqIO.parse is not really a
> substitution for quick_FASTA_reader

OK, I've done that and reworded the docstring.  I agree that Bio.SeqIO is
not a direct substitute for quick_FASTA_reader but they both have their
plus points.

I'll send out an email to the main list about deprecating the following:

Using Bio/SeqUtils as a script
Bio.SeqUtils.apply_on_multi_fasta
Bio.SeqUtils.quicker_apply_on_multi_fasta
Bio.SeqUtils.translate

What about fasta_uniqids? It reads a file but prints to screen which
doesn't seem useful in a python script.

Peter