add entry point to perform chromosome imputation

impute_jass/impute_jass/__main__.py

+import argparse
+import pandas as pd
+from impute_jass.imputation_launcher import ImputationLauncher
+
+
+def launch_chromosome_imputation(args):
+    """
+    Function whose only purpose is to allow the calling of the ImputationLauncher.chromosome_imputation method
+    from an entry point
+    """
+    print(args)
+    imputer = ImputationLauncher( window_size=int(args.window_size), buf=int(args.buffer_size),
+                        lamb= float(args.l2_regularization), pinv_rcond = float(args.eigen_treshold))
+
+    z_file = "{0}/z_{1}_{2}.txt".format(args.zscore_folder, args.gwas, args.chrom)
+    zscore = pd.read_csv(z_file)
+    imputer.chromosome_imputation(args.chrom, zscore, ref_panel, ld_folder)
+
+def add_chromosome_imputation_argument(parser):
+    parser.add_argument('--chrom', required=True, help= "chromosome to impute to the chr\d+ format")
+    parser.add_argument('--gwas', required=True, help= "GWAS to impute to the consortia_trait format")
+
+    parser.add_argument('--ref-folder', required=True, help= "reference panel location (used to determine which snp to impute)")
+    parser.add_argument('--LD-folder', required=True, help= "Location  LD correlation matrices")
+    parser.add_argument('--zscore-folder', required=True, help= "Location of the zscore files of the gwases to impute")
+    parser.add_argument('--output-folder', required=True, help= "Location of the impute zscore files")
+
+    parser.add_argument('--window-size', help= "Size of the non overlapping window", default = 500000)
+    parser.add_argument('--buffer-size', help= "Size of the buffer around the imputation window", default = 125000)
+    parser.add_argument('--l2-regularization', help= "Size of the buffer around the imputation window", default = 0.1)
+    parser.add_argument('--eigen-treshold', help= "treshold under which eigen vectors are removed for the computation of the pseudo inverse", default = 0.1)
+    parser.set_defaults(func=launch_chromosome_imputation)
+    return(parser)
+
+
+def main():
+
+    parser = argparse.ArgumentParser()#prog='impute_jass')
+    parser = add_chromosome_imputation_argument(parser)
+    args = parser.parse_args()
+    args.func(args)
+
+
+if __name__=="__main__":
+    main()

impute_jass/impute_jass/imputation_launcher.py

@@ -7,23 +7,13 @@ 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
 
     """
-    def __init__(self, window_size=10000, imputation_style="online", buf=2500, lamb= 0.01, pinv_rcond = 0.01 ):
+    def __init__(self, window_size=10000, imputation_style="batch", buf=2500, lamb= 0.01, pinv_rcond = 0.01 ):
         """
 
         Args:

impute_jass/setup.py

@@ -10,13 +10,12 @@ setup(name='impute_jass',
       #package_dir = {'': 'jass_preprocessing'},
       packages= ['impute_jass'],
       package_data = {'impute_jass':'./data/*.csv'},
-      zip_safe=False
+      zip_safe=False,
 
-      # entry_points={
-      #     'console_scripts' : [
-      #       'impute_chromosome = imputation_launcher:chromosome_imputation_entry_point'
-      #
-      #     ]
-      # }
+      entry_points={
+          'console_scripts' : [
+            'impute_jass = impute_jass.__main__:main'
+          ]
+      }
 
       )