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fhcrc / deenurp

16S rRNA gene sequence curation and phylogenetic reference set creation
GNU General Public License v3.0
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054 dereplicate refs #56

Closed nhoffman closed 8 years ago

nhoffman commented 8 years ago

Chris,

Can you please review? If you cd tests/filter_outliers && ./run.sh you'll see some pandas warnings - do any of these ring a bell?

/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/indexing.py:284: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  self.obj[key] = _infer_fill_value(value)
/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/indexing.py:461: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy
  self.obj[item] = s
/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/format.py:2190: RuntimeWarning: invalid value encountered in greater
  has_large_values = (abs_vals > 1e6).any()
/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/format.py:2191: RuntimeWarning: invalid value encountered in less
  has_small_values = ((abs_vals < 10**(-self.digits)) &
/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/format.py:2192: RuntimeWarning: invalid value encountered in greater
  (abs_vals > 0)).any()
/fh/fast/fredricks_d/bvdiversity/project-refset-creation/mkrefpkg/src/deenurp/deenurp-env/lib/python2.7/site-packages/pandas/core/ops.py:714: RuntimeWarning: invalid value encountered in less_equal
  result = getattr(x, name)(y)

If it looks ok, can you please merge and release a new version?