python-katlas 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

katlas/__init__.py

@@ -1 +1 @@
-__version__ = "0.0.3"
+__version__ = "0.0.6"

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.dist-info → python_katlas-0.0.7.dist-info}/METADATA

@@ -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
@@ -21,6 +21,7 @@ License-File: LICENSE
 Requires-Dist: statsmodels
 Requires-Dist: fastparquet
 Requires-Dist: tqdm
+Requires-Dist: joblib
 Provides-Extra: dev
 Requires-Dist: nbdev ; extra == 'dev'
 Requires-Dist: pyngrok ; extra == 'dev'

{python_katlas-0.0.5.dist-info → python_katlas-0.0.7.dist-info}/RECORD

@@ -1,14 +1,14 @@
-katlas/__init__.py,sha256=4GZKi13lDTD25YBkGakhZyEQZWTER_OWQMNPoH_UM2c,22
+katlas/__init__.py,sha256=QiiYsv0kcJaB8wCWyT-FnI2b6be87HA-CrrIUn8LQhg,22
 katlas/_modidx.py,sha256=COjpHUccTtv9jU9ifJgAn1uHwwYCpwyyFpM_ifl42Ew,11010
-katlas/core.py,sha256=sJLUQJugXKjN6B71esnYDmB3GcdX8YcFxvfIm1EdrAM,34959
+katlas/core.py,sha256=a4dYSYUSLsixcXmLVJwso3iwHUjlN4XJZ4Vbnr4_I98,35274
 katlas/dl.py,sha256=Rm1EO6oGTiHpqp4EA2xAvbIUnh608FPYOdzndRGKVkc,10849
 katlas/feature.py,sha256=3zgTuCnXqH1e0LGZ2Hkvan852PiaIHxj27cg_TJfKzo,11471
 katlas/imports.py,sha256=-ZphRU8K1KspxMpgRxisE0OskrCw3S8JR8tvmeXBRY0,147
 katlas/plot.py,sha256=vB3gv0aaCNERW1CtdDWqM4jIZOx1auGWwi_1I22xBa0,23630
 katlas/train.py,sha256=s0ucsZVaixCTZPz-XAI2J7zQDeGkiYEJKOc2dFTYsAc,7625
-python_katlas-0.0.5.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-python_katlas-0.0.5.dist-info/METADATA,sha256=rmglXwVjYgVHCpK5wyq8mrRFyv2iyS8ESMD8L3GqEDY,15460
-python_katlas-0.0.5.dist-info/WHEEL,sha256=EVRjI69F5qVjm_YgqcTXPnTAv3BfSUr0WVAHuSP3Xoo,92
-python_katlas-0.0.5.dist-info/entry_points.txt,sha256=SF3xDlCmE84ECTBIMDo_FNg1aXGX2-lXkCvH5o4VgpM,34
-python_katlas-0.0.5.dist-info/top_level.txt,sha256=pKBKw9KOSJgnnFkoilkDij_iJ_tJbIO4XnrSXIleqNc,7
-python_katlas-0.0.5.dist-info/RECORD,,
+python_katlas-0.0.7.dist-info/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+python_katlas-0.0.7.dist-info/METADATA,sha256=azPEmysqMFYpCJlC4gDDA1Yyprb5914xceAysBb7G5Q,15482
+python_katlas-0.0.7.dist-info/WHEEL,sha256=EVRjI69F5qVjm_YgqcTXPnTAv3BfSUr0WVAHuSP3Xoo,92
+python_katlas-0.0.7.dist-info/entry_points.txt,sha256=SF3xDlCmE84ECTBIMDo_FNg1aXGX2-lXkCvH5o4VgpM,34
+python_katlas-0.0.7.dist-info/top_level.txt,sha256=pKBKw9KOSJgnnFkoilkDij_iJ_tJbIO4XnrSXIleqNc,7
+python_katlas-0.0.7.dist-info/RECORD,,