python-katlas 0.0.5__tar.gz → 0.0.7__tar.gz

{python-katlas-0.0.5/python_katlas.egg-info → python-katlas-0.0.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.0.5
+Version: 0.0.7
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/python-katlas
 Author: lily

python-katlas-0.0.7/katlas/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.6"

{python-katlas-0.0.5 → python-katlas-0.0.7}/katlas/core.py

@@ -395,6 +395,7 @@ def predict_kinase(input_string: str, # site sequence
                    ref: pd.DataFrame, # reference dataframe for scoring
                    func: Callable, # function to calculate score
                    to_lower: bool=False, # convert capital STY to lower case
+                   to_upper: bool=False, # convert all letter to uppercase
                    verbose=True
                    ):
     "Predict kinase given a phosphorylation site sequence"
@@ -408,6 +409,10 @@ def predict_kinase(input_string: str, # site sequence
     # If to_lower is True, convert STY in the sequence to lower case
     if to_lower:
         input_string = STY2sty(input_string)
+        
+    # If to_upper is True, convert the sequence to all uppercase
+    if to_upper:
+        input_string = input_string.upper()
     
     results = [] # Initialize a list to store the scores for each kinase
     
@@ -446,10 +451,10 @@ param_PSPA = {'ref':Data.get_pspa_all_norm(), 'func':multiply().func}
 
 # Kinase-substrate dataset, CDDM
 param_CDDM = {'ref':Data.get_cddm(), 'func':sumup}
-param_CDDM_upper = {'ref':Data.get_cddm_upper(), 'func':sumup} # specific for all uppercase
+param_CDDM_upper = {'ref':Data.get_cddm_upper(), 'func':sumup, 'to_upper':True} # specific for all uppercase
 
 # %% ../nbs/00_core.ipynb 46
-def predict_kinase_df(df, seq_col, ref, func, to_lower=False):
+def predict_kinase_df(df, seq_col, ref, func, to_lower=False, to_upper=False):
     print('input dataframe has a length', df.shape[0])
     print('Preprocessing')
     
@@ -466,6 +471,9 @@ def predict_kinase_df(df, seq_col, ref, func, to_lower=False):
     if to_lower:
         df[seq_col] = df[seq_col].apply(STY2sty)
         
+    if to_upper:
+        df[seq_col] = df[seq_col].str.upper()
+        
     # Adjust sequence lengths to match the reference matrix's expected inputs
     max_value = ref.columns.str[:-1].astype(int).max() # Get the highest position index from the reference columns
     min_value = ref.columns.str[:-1].astype(int).min() # Get the lowest position index

{python-katlas-0.0.5 → python-katlas-0.0.7/python_katlas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.0.5
+Version: 0.0.7
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/python-katlas
 Author: lily

{python-katlas-0.0.5 → python-katlas-0.0.7}/python_katlas.egg-info/requires.txt

@@ -1,6 +1,7 @@
 statsmodels
 fastparquet
 tqdm
+joblib
 
 [dev]
 nbdev

{python-katlas-0.0.5 → python-katlas-0.0.7}/settings.ini

@@ -5,7 +5,7 @@
 ### Python library ###
 repo = python-katlas
 lib_name = %(repo)s
-version = 0.0.5
+version = 0.0.7
 min_python = 3.7
 license = apache2
 black_formatting = False
@@ -38,6 +38,6 @@ status = 3
 user = sky1ove
 
 ### Optional ###
-requirements = statsmodels fastparquet tqdm
+requirements = statsmodels fastparquet tqdm joblib
 dev_requirements = nbdev pyngrok fastai>=2.7.12 fastbook fairscale fair-esm logomaker seaborn rdkit umap-learn adjustText bokeh scikit-learn>=1.3.0 openpyxl
 # console_scripts = 

python-katlas-0.0.5/katlas/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.0.3"