update 00_core with new param settings

sky1ove · Feb 19, 2024 · dcc8119 · dcc8119
1 parent 99ea5d8
commit dcc8119
Show file tree

Hide file tree

Showing 2 changed files with 231 additions and 204 deletions.
diff --git a/katlas/core.py b/katlas/core.py
@@ -622,7 +622,7 @@ def predict_kinase(input_string: str, # site sequence
 param3 = {'ref':Data.get_ks(), 'func':sumup, 'to_lower': False}
 param4 = {'ref':Data.get_ks_upper(), 'func':sumup, 'to_lower': False} # specific for all uppercase
 
-# %% ../nbs/00_core.ipynb 70
+# %% ../nbs/00_core.ipynb 71
 def predict_kinase_df(df:pd.DataFrame, # dataframe that contains site sequence
                       seq_col: str, # column name of site sequence
                       ref: pd.DataFrame, # reference df for scoring
@@ -676,7 +676,7 @@ def predict_kinase_df(df:pd.DataFrame, # dataframe that contains site sequence
 
     return out
 
-# %% ../nbs/00_core.ipynb 73
+# %% ../nbs/00_core.ipynb 74
 def get_freq(df_k: pd.DataFrame, # a dataframe for a single kinase that contains phosphorylation sequence splitted by their position
              aa_order = [i for i in 'PGACSTVILMFYWHKRQNDEsty'], # amino acid to include in the full matrix 
              aa_order_paper = [i for i in 'PGACSTVILMFYWHKRQNDEsty'], # amino acid to include in the partial matrix