title: Error message: h5py.h5py_warnings.H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead
body: <p>I'm tring to run <a href="https://mbin.readthedocs.io/en/latest/readme.html" rel="noreferrer">mbin</a> for methylation analysis. But get error message: <code>h5py.h5py_warnings.H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.</code>
  for several attempts, while trying to extract control IPDs with buildcontrols.<br/> 
  Environment:</p>
  
  <ul>
  <li>mbin version: 1.1.1</li>
  <li>Python version:2.7.12 </li>
  <li>Operating System: centOS</li>
  <li>running under virtualenv</li>
  </ul>
  
  <p>I thought it was, again, caused by version.
  What I've tried:
  I tried on a server with both python 3 and 2. And specified virtualenv to use python 2 as interpreter. mbin was successfully installed, but buidlcontrols didn't.</p>
  
  <pre><code>(virtualenv_for_mbin) [yx@localhost virtualenv_for_mbin]$ buildcontrols -i --procs=4 --control_pkl_name=control_means_190201.pkl /data1/yuxiao/userdata1/jobs/016/016504/data/aligned_reads.cmp.h5
  2019-02-01 23:36:31 [INFO] Initiating dictionary of all possible motifs...
  2019-02-01 23:36:31 [INFO]   - Adding 256 4-mer motifs...
  2019-02-01 23:36:31 [INFO] Done: 256 possible contiguous motifs
  
  2019-02-01 23:36:31 [INFO]   - Adding 1024 5-mer motifs...
  2019-02-01 23:36:31 [INFO] Done: 1536 possible contiguous motifs
  
  2019-02-01 23:36:31 [INFO]   - Adding 4096 6-mer motifs...
  2019-02-01 23:36:32 [INFO] Done: 7680 possible contiguous motifs
  
  2019-02-01 23:36:32 [INFO]   - Adding bipartite motifs to search space...
  2019-02-01 23:36:33 [INFO] Done: 194560 possible bipartite motifs
  
  2019-02-01 23:36:33 [INFO] 
  2019-02-01 23:36:33 [INFO] Preparing to create new control data in ctrl_tmp
  Traceback (most recent call last):
    File "/data2/Software/virtualenv_for_mbin/bin/buildcontrols", line 10, in &lt;module&gt;
      sys.exit(launch())
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 20, in launch
      extract_controls(opts, control_aln_fn)
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 40, in extract_controls
      opts           = controls.scan_WGA_aligns()
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 352, in scan_WGA_aligns
      reader = openIndexedAlignmentFile(self.control_aln_fn)
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/pbcore/io/opener.py", line 52, in openIndexedAlignmentFile
      return CmpH5Reader(fname, sharedIndex=sharedIndex)
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/pbcore/io/align/CmpH5IO.py", line 729, in __init__
      self._loadAlignmentInfo(sharedIndex)
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/pbcore/io/align/CmpH5IO.py", line 745, in _loadAlignmentInfo
      rawAlignmentIndex = self.file["/AlnInfo/AlnIndex"].value
    File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
    File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
    File "/data2/Software/virtualenv_for_mbin/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 313, in value
      "Use dataset[()] instead.", H5pyDeprecationWarning)
  h5py.h5py_warnings.H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
  </code></pre>
  
  <p>I checked python version:</p>
  
  <pre><code>(virtualenv_for_mbin) [yx@localhost virtualenv_for_mbin]$ python -V
  Python 3.6.5 :: Anaconda, Inc.
  </code></pre>
  
  <p>So, I immediately tried to run a new virtualenv.</p>
  
  <pre><code>[yx@localhost Software]$ mkdir venv_tmp
  [yx@localhost Software]$ cd venv_tmp/
  [yx@localhost venv_tmp]$ virtualenv --python=/usr/local/bin/python2.7 .
  Running virtualenv with interpreter /usr/local/bin/python2.7
  New python executable in /data2/Software/venv_tmp/bin/python2.7
  Also creating executable in /data2/Software/venv_tmp/bin/python
  Installing setuptools, pip, wheel...
  done.
  [yx@localhost venv_tmp]$ . bin/activate
  (venv_tmp) [yx@localhost venv_tmp]$ python -V
  Python 3.6.5 :: Anaconda, Inc.
  </code></pre>
  
  <p>Then, I turned to another server.....with only python 2.7 installed.</p>
  
  <pre><code>(venv_for_mbin) [yuxiao@localhost data_tmp]$ buildcontrols -i --procs=4 --control_pkl_name=control_means_190202.pkl aligned_reads.cmp.h5
  2019-02-02 11:06:16 [INFO] Initiating dictionary of all possible motifs...
  2019-02-02 11:06:16 [INFO]   - Adding 256 4-mer motifs...
  2019-02-02 11:06:16 [INFO] Done: 256 possible contiguous motifs
  
  2019-02-02 11:06:16 [INFO]   - Adding 1024 5-mer motifs...
  2019-02-02 11:06:16 [INFO] Done: 1536 possible contiguous motifs
  
  2019-02-02 11:06:16 [INFO]   - Adding 4096 6-mer motifs...
  2019-02-02 11:06:16 [INFO] Done: 7680 possible contiguous motifs
  
  2019-02-02 11:06:16 [INFO]   - Adding bipartite motifs to search space...
  2019-02-02 11:06:18 [INFO] Done: 194560 possible bipartite motifs
  
  2019-02-02 11:06:18 [INFO] 
  2019-02-02 11:06:18 [INFO] Preparing to create new control data in ctrl_tmp
  Traceback (most recent call last):
    File "/data1/yuxiao/venv_for_mbin/bin/buildcontrols", line 10, in &lt;module&gt;
      sys.exit(launch())
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 20, in launch
      extract_controls(opts, control_aln_fn)
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 40, in extract_controls
      opts           = controls.scan_WGA_aligns()
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/mbin/controls.py", line 352, in scan_WGA_aligns
      reader = openIndexedAlignmentFile(self.control_aln_fn)
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/pbcore/io/opener.py", line 52, in openIndexedAlignmentFile
      return CmpH5Reader(fname, sharedIndex=sharedIndex)
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/pbcore/io/align/CmpH5IO.py", line 729, in __init__
      self._loadAlignmentInfo(sharedIndex)
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/pbcore/io/align/CmpH5IO.py", line 745, in _loadAlignmentInfo
      rawAlignmentIndex = self.file["/AlnInfo/AlnIndex"].value
    File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper
    File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper
    File "/data1/yuxiao/venv_for_mbin/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 313, in value
      "Use dataset[()] instead.", H5pyDeprecationWarning)
  h5py.h5py_warnings.H5pyDeprecationWarning: dataset.value has been deprecated. Use dataset[()] instead.
  (venv_for_mbin) [yuxiao@localhost data_tmp]$ python -V
  Python 2.7.12
  </code></pre>
  
  <p>Still got the same error message. And I'm here hoping someone can help me. Thx a lot.</p>