[Biopython-dev] Use of depreciated string functions

[Bruce Southey]

Peter wrote:
> On Mon, Nov 24, 2008 at 5:47 PM, Bruce Southey <bsouthey at gmail.com> wrote:
>   
>>> Once I've dealt with Biopython 1.49, I'd be happy to look at a patch
>>> to remove more "import string" usage from non-obsolete, non-deprecated
>>> code.  It would be a little risky doing this to modules without unit
>>> tests, but that's another area you've shown some interest in anyway...
>>>
>>> Thanks,
>>>
>>> Peter
>>>       
>> Hi,
>> I was planning to get started on with these depending on what time I have
>> available. So just a quick question:
>> Do you want one bug report per patch per file?
>> Or just let me know if there is another way.
>>     
>
> I'd suggest one general bug, and uploading one patch per module - that
> way the can be evaluated on a case by case basis (a single huge
> multi-file patch would be more difficult, and could become out of
> date).
>
> Personally however, I would prioritise more unit test coverage over
> this, but on the other hand its the kind of short task you can handle
> when you have the odd spare 10 minutes.  Up to you.
>
> Peter
>   
Hi,
I have filed Bug 2688 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2688> as a general bug for 
the files in the Bio module that use the depreciated string functions. I 
listed all the files that I identified that imported string and whether 
or not I provided a patch for it. Bug  2683 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2683> lists those files 
that import string but do not use it.

There is one attachment for each file (excluding mistakes).

In addition, Bugs 2684 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2684> and 2685 
<http://bugzilla.open-bio.org/show_bug.cgi?id=2685> were created because 
these involve rewritten code that was related to this. I probably should 
have created a separate one for
 SubsMat/FreqTable.py although the reason directly involves the string 
module.

Regards
Bruce