Merge pull request #78 from ArcInstitute/dev

fix a bug in `filterLowCounts`

screenpro/__init__.py

@@ -28,6 +28,6 @@
 from .ngs import GuideCounter
 from .assays import PooledScreens, GImaps
 
-__version__ = "0.4.4"
+__version__ = "0.4.5"
 __author__ = "Abe Arab"
 __email__ = '[email protected]' # "[email protected]"

screenpro/assays.py

@@ -86,7 +86,7 @@ def _calculateGrowthFactor(self, untreated, treated, db_rate_col):
 
         return out
 
-    def filterLowCounts(self, filter_type='sum', minimum_reads=50):
+    def filterLowCounts(self, filter_type='all', minimum_reads=50):
         """
         Filter low counts in adata.X
         """

screenpro/preprocessing.py

@@ -9,7 +9,7 @@ def findLowCounts(adata, filter_type, minimum_reads, verbose=True):
 
     Parameters:
         adata (AnnData): AnnData object containing the counts to be filtered.
-        filter_type (str): specify the filter type. Possible values are: 'either', 'all', or 'sum'.
+        filter_type (str): specify the filter type. Possible values are: 'all', or 'sum'.
         minimum_reads (int): minimum number of reads.
         verbose (bool): print the number of removed variables. Default is True.
 
@@ -18,14 +18,12 @@ def findLowCounts(adata, filter_type, minimum_reads, verbose=True):
     """
     count_bin = adata.X >= minimum_reads
 
-    if filter_type == 'either':
-        out = adata[:, ~(~count_bin.all(axis=0))].copy()
-    elif filter_type == 'all':
+    if filter_type == 'all':
         out = adata[:, count_bin.all(axis=0)].copy()
     elif filter_type == 'sum':
         out = adata[:, adata.to_df().sum(axis=0) >= minimum_reads].copy()
     else:
-        raise ValueError(f'filter_type "{filter_type}" not recognized. Use "either", "all", or "sum".')
+        raise ValueError(f'filter_type "{filter_type}" not recognized. Use "all", or "sum".')
 
     if verbose:
         n_removed = adata.shape[1] - out.shape[1]