adding main file

impute_jass/impute_jass/imputation_launcher.py

@@ -6,6 +6,18 @@ import glob
 import pandas as pd
 from .windows import ld_region_centered_window_imputation, impg_like_imputation, realigned_zfiles_on_panel
 
+
+def chromosome_imputation_entry_point(chrom, zscore, ref_panel, ld_folder, window_size=10000, imputation_style="online", buf=2500, lamb= 0.01, pinv_rcond = 0.01):
+    """
+    Function whose only purpose is to allow the calling of the ImputationLauncher.chromosome_imputation method
+    from an entry point
+    """
+    imputer = ImputationLauncher( window_size=10000, imputation_style="online", buf=2500, lamb= 0.01, pinv_rcond = 0.01)
+    imputer.chromosome_imputation(chrom, zscore, ref_panel, ld_folder)
+
+
+
+
 class ImputationLauncher(object):
     """
     Class perform imputation of snp from summary statistic

impute_jass/impute_jass/stat_models.py

@@ -28,7 +28,7 @@ def impg_model(zt, sig_t, sig_i_t, lamb=0.01, rcond=0.01,  batch=True):
     """
     sig_t = sig_t.values
     np.fill_diagonal(sig_t, (1+lamb))
-    sig_t_inv = sc.linalg.pinv(sig_t)#, rcond=rcond)
+    sig_t_inv = sc.linalg.pinv(sig_t, rcond=rcond)
 
     if batch:
         condition_number = np.array([np.linalg.cond(sig_t)]*sig_i_t.shape[0])

impute_jass/setup.py

@@ -12,11 +12,11 @@ setup(name='impute_jass',
       package_data = {'impute_jass':'./data/*.csv'},
       zip_safe=False
 
-      entry_points={
-          'console_scripts' : [
-            'impute_chromosome = '
-
-          ]                              
-      }
+      # entry_points={
+      #     'console_scripts' : [
+      #       'impute_chromosome = imputation_launcher:chromosome_imputation_entry_point'
+      #
+      #     ]
+      # }
 
       )