change index type option name

jass_preprocessing/__main__.py

@@ -95,7 +95,7 @@ def add_preprocessing_argument():
     parser.add_argument('--additional-masked-region', required=False, help= "List of dictionary containing coordinate of region to mask. For example :[{'chr':6, 'start':50000000, 'end': 70000000}, {'chr':6, 'start':100000000, 'end': 120000000}]", default='None')
 
     parser.add_argument('--imputation-quality-treshold', required=False, help= "minimum imputation quality in summary statistics", default='None')
-    parser.add_argument('--index-type', required=False, help= "type of index : rsID or chr:postion:ref_allele:alt_allele", default='rsid')
+    parser.add_argument('--index-type', required=False, help= "type of index : rsID or chr:postion:ref_allele:alt_allele", default='rs-number')
 
     parser.set_defaults(func=launch_preprocessing)
 

jass_preprocessing/map_reference.py

@@ -15,7 +15,7 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
         Filter the reference panel by  minimum allele frequency (hg19 coordinate)
         minimum_MAF (float): minimum allele frequency for a SNPs to be retain in the panel
         region_to_mask (dict): a list of additional regions to mask
-        type_of_index(str): 'rsid' or 'positional'
+        type_of_index(str): 'rs-number' or 'positional'
     Return:
         ref (pandas dataframe): the reference_panel with the specified filter applied
     """
@@ -44,7 +44,7 @@ def read_reference(gwas_reference_panel, mask_MHC=False, minimum_MAF=None, regio
 
 
 
-def map_on_ref_panel(gw_df , ref_panel, index_type="rsid"):
+def map_on_ref_panel(gw_df , ref_panel, index_type="rs-number"):
     """
     Merge Gwas dataframe with the reference panel
     Make sure that the same SNPs are in the reference panel and the gwas
@@ -58,7 +58,7 @@ def map_on_ref_panel(gw_df , ref_panel, index_type="rsid"):
     """
 
 
-    if index_type=="rsid":
+    if index_type=="rs-number":
         merge_GWAS = pd.merge(ref_panel, gw_df,
                             how='inner', indicator=True, left_index=True, right_index=True)
         print("SNPs {}".format(merge_GWAS.shape[0]))
@@ -80,7 +80,7 @@ def map_on_ref_panel(gw_df , ref_panel, index_type="rsid"):
             print(merge_GWAS)
             merge_GWAS.set_index("snp_id", inplace=True)
         else:
-            raise ValueError("index_type can take only two values: 'rsid' or 'positional'")
+            raise ValueError("index_type can take only two values: 'rs-number' or 'positional'")
 
     if (("pos" in merge_GWAS.columns) and ("POS" in merge_GWAS.columns))
         if (merge_GWAS.pos == merge_GWAS.POS).mean()> 0.95):