python-katlas 0.0.9__tar.gz → 0.1.0__tar.gz

{python-katlas-0.0.9/python_katlas.egg-info → python-katlas-0.1.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.0.9
+Version: 0.1.0
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/python-katlas
 Author: lily

python-katlas-0.1.0/katlas/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.0.9"

{python-katlas-0.0.9 → python-katlas-0.1.0}/katlas/core.py

@@ -451,17 +451,18 @@ def predict_kinase(input_string: str, # site sequence
 
 # %% ../nbs/00_core.ipynb 41
 # PSPA
-param_PSPA_st = {'ref':Data.get_pspa_st_norm(), 'func':multiply} # Johnson et al. Nature official
-param_PSPA_y = {'ref':Data.get_pspa_tyr_norm(), 'func':multiply}
-param_PSPA = {'ref':Data.get_pspa_all_norm(), 'func':multiply}
+param_PSPA_st = {'ref':Data.get_pspa_st_norm().astype('float32'), 'func':multiply} # Johnson et al. Nature official
+param_PSPA_y = {'ref':Data.get_pspa_tyr_norm().astype('float32'), 'func':multiply}
+param_PSPA = {'ref':Data.get_pspa_all_norm().astype('float32'), 'func':multiply}
 
 
 # Kinase-substrate dataset, CDDM
-param_CDDM = {'ref':Data.get_cddm(), 'func':sumup}
-param_CDDM_upper = {'ref':Data.get_cddm_upper(), 'func':sumup, 'to_upper':True} # specific for all uppercase
+param_CDDM = {'ref':Data.get_cddm().astype('float32'), 'func':sumup}
+param_CDDM_upper = {'ref':Data.get_cddm_upper().astype('float32'), 'func':sumup, 'to_upper':True} # specific for all uppercase
 
-# %% ../nbs/00_core.ipynb 45
+# %% ../nbs/00_core.ipynb 46
 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')
     
@@ -493,12 +494,20 @@ def predict_kinase_df(df, seq_col, ref, func, to_lower=False, to_upper=False):
     df['keys'] = df['site_seq'].apply(get_dict)
     input_keys_df  = df[['keys']].explode('keys').reset_index()
     input_keys_df.columns = ['input_index', 'key']
+    
+    
     ref_T = ref.T
     
-    merged_df = input_keys_df.merge(ref_T, left_on='key', right_index=True, how='inner')
+    input_keys_df = input_keys_df.set_index('key')
+    
+    
+    print('Merging reference')
+    merged_df = input_keys_df.merge(ref_T, left_index=True, right_index=True, how='inner')
+
+    print('Finish merging')
     
     if func == sumup:
-        grouped_df = merged_df.drop(columns=['key']).groupby('input_index').sum()
+        grouped_df = merged_df.groupby('input_index').sum()
         out = grouped_df.reindex(df.index)
          
     elif func==multiply:
@@ -514,7 +523,7 @@ def predict_kinase_df(df, seq_col, ref, func, to_lower=False, to_upper=False):
             kinase_df = kinase_df.rename(columns={kinase: 'value'})
 
             # Compute log_value
-            kinase_df['log_value'] = np.log2(kinase_df['value'],where=kinase_df['value']>0)
+            kinase_df['log_value'] = np.log2(kinase_df['value'].where(kinase_df['value'] > 0))
 
             # Group by 'input_index' and compute sum and count
             grouped = kinase_df.dropna().groupby('input_index')
@@ -541,7 +550,7 @@ def predict_kinase_df(df, seq_col, ref, func, to_lower=False, to_upper=False):
     # Return results as a DataFrame
     return out
 
-# %% ../nbs/00_core.ipynb 54
+# %% ../nbs/00_core.ipynb 56
 def get_pct(site,ref,func,pct_ref):
     
     "Replicate the precentile results from The Kinase Library."
@@ -566,7 +575,7 @@ def get_pct(site,ref,func,pct_ref):
     final.columns=['log2(score)','percentile']
     return final
 
-# %% ../nbs/00_core.ipynb 60
+# %% ../nbs/00_core.ipynb 62
 def get_pct_df(score_df, # output from predict_kinase_df 
                pct_ref, # a reference df for percentile calculation
               ):
@@ -591,7 +600,7 @@ def get_pct_df(score_df, # output from predict_kinase_df
     
     return percentiles_df
 
-# %% ../nbs/00_core.ipynb 65
+# %% ../nbs/00_core.ipynb 67
 def get_unique_site(df:pd.DataFrame = None,# dataframe that contains phosphorylation sites
                     seq_col: str='site_seq', # column name of site sequence
                     id_col: str='gene_site' # column name of site id
@@ -607,7 +616,7 @@ def get_unique_site(df:pd.DataFrame = None,# dataframe that contains phosphoryla
     
     return unique
 
-# %% ../nbs/00_core.ipynb 68
+# %% ../nbs/00_core.ipynb 70
 def extract_site_seq(df: pd.DataFrame, # dataframe that contains protein sequence
                      seq_col: str, # column name of protein sequence
                      position_col: str # column name of position 0
@@ -633,7 +642,7 @@ def extract_site_seq(df: pd.DataFrame, # dataframe that contains protein sequenc
         
     return np.array(data)
 
-# %% ../nbs/00_core.ipynb 73
+# %% ../nbs/00_core.ipynb 75
 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
@@ -674,7 +683,7 @@ def get_freq(df_k: pd.DataFrame, # a dataframe for a single kinase that contains
     
     return paper,full
 
-# %% ../nbs/00_core.ipynb 77
+# %% ../nbs/00_core.ipynb 79
 def query_gene(df,gene):
     
     "Query gene in the phosphoproteomics dataset"
@@ -688,7 +697,7 @@ def query_gene(df,gene):
     
     return df_gene
 
-# %% ../nbs/00_core.ipynb 81
+# %% ../nbs/00_core.ipynb 83
 def get_ttest(df, 
               columns1, # list of column names for group1
               columns2, # list of column names for group2
@@ -758,7 +767,7 @@ def get_ttest(df,
     
     return results
 
-# %% ../nbs/00_core.ipynb 82
+# %% ../nbs/00_core.ipynb 84
 def get_metaP(p_values):
     
     "Use Fisher's method to calculate a combined p value given a list of p values; this function also allows negative p values (negative correlation)"
@@ -770,7 +779,7 @@ def get_metaP(p_values):
 
     return score
 
-# %% ../nbs/00_core.ipynb 85
+# %% ../nbs/00_core.ipynb 87
 def raw2norm(df: pd.DataFrame, # single kinase's df has position as index, and single amino acid as columns
              PDHK: bool=False, # whether this kinase belongs to PDHK family 
             ):
@@ -793,7 +802,7 @@ def raw2norm(df: pd.DataFrame, # single kinase's df has position as index, and s
     
     return df2
 
-# %% ../nbs/00_core.ipynb 87
+# %% ../nbs/00_core.ipynb 89
 def get_one_kinase(df: pd.DataFrame, #stacked dataframe (paper's raw data)
                    kinase:str, # a specific kinase
                    normalize: bool=False, # normalize according to the paper; special for PDHK1/4

{python-katlas-0.0.9 → python-katlas-0.1.0/python_katlas.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: python-katlas
-Version: 0.0.9
+Version: 0.1.0
 Summary: tools for predicting kinome specificities
 Home-page: https://github.com/sky1ove/python-katlas
 Author: lily

{python-katlas-0.0.9 → python-katlas-0.1.0}/settings.ini

@@ -5,7 +5,7 @@
 ### Python library ###
 repo = python-katlas
 lib_name = %(repo)s
-version = 0.0.9
+version = 0.1.0
 min_python = 3.7
 license = apache2
 black_formatting = False

python-katlas-0.0.9/katlas/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.0.8"