[Biopython-dev] [Bug 2867] New: 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

           Summary: Bio.PDB.PDBList.update_pdb calls invalid os.cmd
           Product: Biopython
           Version: 1.51b
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mlrodrigues at igc.gulbenkian.pt


As listed in the traceback, this module tries to use an invalid function from
the os module.

Traceback (most recent call last):
  File "update_pdb.py", line 33, in <module>
    update(pdblist, my_try)
  File "update_pdb.py", line 27, in update
    x.update_pdb()
  File "/usr/lib/pymodules/python2.5/Bio/PDB/PDBList.py", line 280, in
update_pdb
    os.cmd('mv %s %s'%(old_file,new_file))
AttributeError: 'module' object has no attribute 'cmd'


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