[Biopython-dev] Bio.Ais

[Michiel de Hoon]

Since no users came forward, I deprecated Bio.Ais and removed the corresponding test_ais.py. I added a statement in the DeprecationWarning that this module is on the nomination to be removed (in some future Biopython release), if no users come forward.

--Michiel.

Michiel de Hoon <mjldehoon at yahoo.com> wrote: Looking at this again, currently we have no documentation for Bio.Ais, no maintainer, and no apparent users (at least, I couldn't find any in the mailing list archives). Would anybody mind very much if I mark this module as deprecated?
Just to find out if there are any users of this code out there.

--Michiel.

Michiel de Hoon  wrote: Hi everybody,

I was checking which Biopython modules access Entrez/GenBank in any way, and in the process found the script example_ais2.py in Bio/Ais/Examples (this is not related to Entrez/GenBank in any way, it just caught my eye because it imports urllib). 
Currently, this example script does not seem to work:

$ python example_ais2.py
Traceback (most recent call last):
  File "example_ais2.py", line 39, in 
    immune = Immune( align, alphabet, 100 )
...
TypeError: 'int' object is not iterable

The directory Bio/Ais/Examples and its file example_ais2.py only appears in CVS and is not included in Biopython releases.

Does anybody know how to fix this example? If not, what should we do with it?

--Michiel.

       
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