Update save_output.py

jass_preprocessing/save_output.py

@@ -12,19 +12,22 @@ def save_output_by_chromosome(mgwas, ImpG_output_Folder, my_study):
     mgwas_copy.dropna(subset=["computed_z"], how="any", inplace=True)
     print(mgwas_copy.index.unique())
     for chrom in mgwas_copy.index.unique():
-        print(mgwas_copy.loc[chrom])
-        mgwas_chr = pd.DataFrame({
-                        'rsID': mgwas_copy.loc[chrom].snp_id,
-                        'pos': mgwas_copy.loc[chrom].pos,
-                        'A0': mgwas_copy.loc[chrom].ref,
-                        'A1':mgwas_copy.loc[chrom].alt,
-                        'Z': mgwas_copy.loc[chrom].computed_z,
-                        'P': mgwas_copy.loc[chrom].pval
-            }, columns= ['rsID', 'pos', 'A0', "A1", "Z", "P" ])
-
-        impg_output_file = ImpG_output_Folder + 'z_'+ my_study +'_chr'+str(chrom)+".txt"
-        print("WRITING CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
-        mgwas_chr.sort_values(by="pos").to_csv(impg_output_file, sep="\t", index=False)
+        if type(mgwas_copy.loc[chrom]) is pd.core.frame.DataFrame:
+            print(mgwas_copy.loc[chrom])
+            mgwas_chr = pd.DataFrame({
+                            'rsID': mgwas_copy.loc[chrom].snp_id,
+                            'pos': mgwas_copy.loc[chrom].pos,
+                            'A0': mgwas_copy.loc[chrom].ref,
+                            'A1':mgwas_copy.loc[chrom].alt,
+                            'Z': mgwas_copy.loc[chrom].computed_z,
+                            'P': mgwas_copy.loc[chrom].pval
+                }, columns= ['rsID', 'pos', 'A0', "A1", "Z", "P" ])
+
+            impg_output_file = ImpG_output_Folder + 'z_'+ my_study +'_chr'+str(chrom)+".txt"
+            print("WRITING CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
+            mgwas_chr.sort_values(by="pos").to_csv(impg_output_file, sep="\t", index=False)
+        else:
+            print("NO or 1 value for CHR {} results for {} to: {}".format(chrom, my_study, ImpG_output_Folder))
 
 
 def save_output(mgwas, ImpG_output_Folder, my_study):