[BioPython] Deprecated Bio.sequtils

[Frank Kauff]

Hi Brad,

while you're at it... :-)

there seems to be a little bug in
SeqUtils.quicker_apply_on_multi_fasta()

Instead of 

if result:
     results.append('>%s\n%s' % (record.title, result))

it should be

if result:
     results.append('>%s\n%s' % (name, result))
 
Probably a copy-paste error from apply_on_multi_fasta()

Cheers,
Frank


On Fri, 2004-04-02 at 11:28, Brad Chapman wrote:
> Hello everyone;
> In checking into a bug report, I suddenly realized for the first
> time that Bio/sequtils.py and Bio/SeqUtils/__init__.py duplicate the
> same code. It looks like sequtils.py was expanded to an entire
> directory at some point but the duplication was never removed. Even
> worse, there have been different fixes and additions to both parts.
> 
> To fix this problem, I've merged all the changes into
> Bio/SeqUtils/__init__.py and officially deprecated Bio/sequtils.py.
> The SeqUtils directory contains other useful manipulation code so
> this seems the right way to do things without being too confusing.
> 
> For now Bio/sequtils.py raises a DeprecationWarning when used, but
> still works (by importing the code from Bio/SeqUtils.py into it's
> namespace. This will give people time to update their scripts
> without breaking anything. To fix Scripts that reference
> Bio/sequtils.py you need to change:
> 
> from Bio.sequtils import whatever
> 
> to:
> 
> from Bio.SeqUtils import whatever
> 
> Sorry about any difficulties this may cause. Bio/sequtils.py will
> remain around for a while to maintain back compatibility with the
> warning. Please let me know if I've done anything which does not
> leave it back compatible.
> 
> Thanks!
> Brad
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-- 
Frank Kauff
Dept. of Biology
Duke University
Box 90338
Durham, NC 27708
USA

Phone 919-660-7382
Fax 919-660-7293