Merge pull request #67 from ArcInstitute/cli

Fix bugs and improve code

screenpro/__init__.py

@@ -6,9 +6,9 @@
 from . import load
 from . import dashboard
 
-from .ngs import Counter
+from .ngs import GuideCounter
 from .assays import PooledScreens, GImaps
 
-__version__ = "0.3.4"
+__version__ = "0.3.5"
 __author__ = "Abe Arab"
 __email__ = '[email protected]' # "[email protected]"

screenpro/assays.py

@@ -147,7 +147,8 @@ def calculateDrugScreen(self, t0, untreated, treated, db_untreated, db_treated,
             runPhenoScoreForReplicate(
                 self.adata, x_label = x_label, y_label = y_label, score = score_label,
                 transformation=self.fc_transformation, 
-                growth_factor_table=growth_factor_table
+                growth_factor_table=growth_factor_table,
+                **kwargs
             ).add_prefix(f'{score_label}_')
 
             for x_label, y_label, score_label in [
@@ -190,15 +191,15 @@ def calculateFlowBasedScreen(self, low_bin, high_bin, score_level, run_name=None
         # save phenotype name for reference
         self._add_phenotype_results(f'delta:{delta_name}')
 
-    def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
+    def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_label='control', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
         """
         Get phenotype scores for a given score level
 
         Args:
             run_name (str): name of the phenotype calculation run to retrieve
             score_name (str): name of the score to retrieve, e.g. 'gamma', 'tau', 'rho', 'delta'
             threshold (float): threshold for filtering significant hits, default is 5
-            ctrl_label (str): label for the negative control, default is 'negCtrl'
+            ctrl_label (str): label for the negative control, default is 'control'
             target_col (str): column name for the target gene, default is 'target'
             pvalue_column (str): column name for the p-value, default is 'ttest pvalue'
             score_column (str): column name for the score, default is 'score'
@@ -243,7 +244,7 @@ def getPhenotypeScores(self, score_name, run_name='auto', threshold=5, ctrl_labe
 
         return out
 
-    def getAnnotatedTable(self, run_name='auto', threshold=5, ctrl_label='negCtrl', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
+    def getAnnotatedTable(self, run_name='auto', threshold=5, ctrl_label='control', target_col='target',pvalue_column='ttest pvalue', score_column='score'):
         hit_dict = {
             'gamma':{
                 'up_hit':'up_hit',

screenpro/load.py

@@ -20,7 +20,8 @@ def load_cas9_sgRNA_library(library_path, library_type, sep='\t', index_col=0, p
 
     ## Evaluate library table and reformat columns for downstream analysis
     # I would like to name the target column 'target' if it is named 'gene'!
-
+    #TODO: Add option to keep sublibrary column!
+
     if library_type == "single_guide_design":
         eval_columns = ['target', 'sgID', 'protospacer', 'sequence']