[Biopython-dev] Cleaning up Bio.SeqUtils

[Thomas Sicheritz-Ponten]

Hej all,

as I am guilty for most of the functions in SeqUtils/__init__.py, I 
might as well join the cleaning team ...

apply_on_multi_fasta and quicker_apply_on_multi_fasta were only 
functions to the turn the original SeqUtils.py into a possible 
standalone program, but I guess not many actually used it.
On the other hand quick_FASTA_reader was and still is used by a lot of 
people, despite the irritating splitting bug which occurs if an entry 
name happens to contain '>' ...

Also, the translate and complement functions are from the time were 
these functions were not easily accessed (we are talking about 2001-2002)

In my opinion, apply_on_multi_fasta, quicker_apply_on_multi_fasta and 
the redundant translation machinery could and should get removed. Also 
if one can change the split function in quick_FASTA_reader? (I don't 
have had checkin access since a long time)

Are there any other dubios functions we should discuss?

cheers
-thomas

-- 
Sicheritz-Ponten Thomas, Associate Professor, Ph.D       (
Head of Metagenomics, Technical University of Denmark     \
Center for Biological Sequence Analysis, BioCentrum        )
CBS: +45 45 252422      Building 208, DK-2800 Lyngby  ##----->
Fax: +45 45 931585      http://www.cbs.dtu.dk/~thomas      )
                                                           /
      ... damn arrow eating trees ...                     (


Peter wrote:
> Dear all,
> 
> I've previously mentioned the idea of cleaning up
> Bio/SeqUtils/__init__.py in passing.  I've been reminded about this by
> Bug 2585 where Sebastian spotted a problem in one of the FASTA related
> functions.
> http://bugzilla.open-bio.org/show_bug.cgi?id=2585
> 
> I've updated the docstrings in CVS to describe the three functions
> quick_FASTA_reader, apply_on_multi_fasta and
> quicker_apply_on_multi_fasta as obsolete but I would like to suggest
> going further and deprecating them.
> 
> There are other dubious or redundant functions in
> Bio/SeqUtils/__init__.py such as a translate function.  Again, would
> there be any objection to deprecating this too?
> 
> Peter
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