[Biopython-dev] Cleaning up Bio.SeqUtils

[Peter]

On Thu, Sep 25, 2008 at 7:57 PM, Thomas Sicheritz-Ponten
<thomas at cbs.dtu.dk> wrote:
> Hej all,
>
> as I am guilty for most of the functions in SeqUtils/__init__.py, I might as
> well join the cleaning team ...

Excellent :)

> 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.

That would explain some of that module's style.  We could deprecate
the standalone bit too when we deprecate these functions.

> 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 '>' ...

We should probably fix that if you think it can be done without
loosing the current simplicity and speed (see below).

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

That does make sense - its a shame with hindsight that Biopython ended
up with several ways to do this.

> In my opinion, apply_on_multi_fasta, quicker_apply_on_multi_fasta and the
> redundant translation machinery could and should get removed.

OK.  We should probably ask on the main list as a courtesy, and then
deprecate them for the next release.

> Also if one can change the split function in quick_FASTA_reader? (I don't
> have had checkin access since a long time)

If this is just an expired account / lost password you could try
emailing the OBF support guys directly.  If they need someone to vouch
for you drop me or Michiel an email off list.  In the short term I'm
happy to check in a patch on your behalf (by email or via a bug
report).

> Are there any other dubios functions we should discuss?

I'm sure there are more - but that should keep us busy for now :)

Are you happy with my recent tweak to the seq3 function (CVS revision
1.15)?  I wasn't 100% sure why it had used "Xer"

http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/SeqUtils/__init__.py.diff?r1=1.14&r2=1.15&cvsroot=biopython

Thanks,

Peter