[Biopython-dev] [Bug 2867] Bio.PDB.PDBList.update_pdb calls invalid os.cmd

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2867





------- Comment #2 from biopython-bugzilla at maubp.freeserve.co.uk  2009-07-21 17:09 EST -------
I've checked a fix for this into CVS, but have not tested it.
Could you update and retry?

It might be simplest to reinstall all of Biopython from CVS or github,
but you only need to update this one file,
/usr/lib/pymodules/python2.5/Bio/PDB/PDBList.py

The new version will be on github soon, or here soon:
http://biopython.org/SRC/biopython/Bio/PDB/PDBList.py

The differences are quite small:

RCS file: /home/repository/biopython/biopython/Bio/PDB/PDBList.py,v
retrieving revision 1.25
diff -r1.25 PDBList.py
37a38
> #TODO - Use os.path.join(...) instead of adding strings with os.sep
39a41
> import shutil
248d249
< 
280c281
<         os.cmd('mv %s %s'%(old_file,new_file))
---
>         shutil.move(old_file, new_file)


i.e. The new version uses shutil.move(old_file, new_file) instead.

Thanks!

Peter


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