explicitly convert chromosome and basepairs to int for df indices

Author: omerwe

ldsc_polyfun/parse.py

@@ -37,7 +37,9 @@ def set_snpid_index(df):
     df.loc[df['A1_first'], 'A1s'] = df.loc[df['A1_first'], 'A1'].copy()
     df['A2s'] = df['A1'].copy()
     df.loc[df['A1_first'], 'A2s'] = df.loc[df['A1_first'], 'A2'].copy()
-    df.index = df['CHR'].astype(str) + '.' + df['BP'].astype(str) + '.' + df['A1s'] + '.' + df['A2s']
+    s_chr = df['CHR'].map(lambda c: int(c) if str(c)[0] in ['0','1','2','3','4','5,','6','7','8','9'] else c).astype(str)
+    s_bp = df['BP'].astype(int).astype(str)
+    df.index = s_chr + '.' + s_bp + '.' + df['A1s'] + '.' + df['A2s']
     df.index.name = 'snpid'
     df.drop(columns=['A1_first', 'A1s', 'A2s'], inplace=True)
     return df

polyfun_utils.py

@@ -67,7 +67,9 @@ def set_snpid_index(df, copy=False, allow_duplicates=False, allow_swapped_indel_
     df.loc[df['A1_first'], 'A1s'] = df.loc[df['A1_first'], 'A1'].copy()
     df['A2s'] = df['A1'].copy()
     df.loc[df['A1_first'], 'A2s'] = df.loc[df['A1_first'], 'A2'].copy()
-    df.index = df['CHR'].astype(int).astype(str) + '.' + df['BP'].astype(str) + '.' + df['A1s'] + '.' + df['A2s']
+    s_chr = df['CHR'].map(lambda c: int(c) if str(c)[0] in ['0','1','2','3','4','5,','6','7','8','9'] else c).astype(str)
+    s_bp = df['BP'].astype(int).astype(str)
+    df.index = s_chr + '.' + s_bp + '.' + df['A1s'] + '.' + df['A2s']
     df.index.name = 'snpid'
     df.drop(columns=['A1_first', 'A1s', 'A2s'], inplace=True)
 

test_polyfun.py

@@ -249,7 +249,7 @@ def test_finemapper_susie(tmpdir, python3_exe):
     #print(finemapper_cmd)
     retval = os.system(finemapper_cmd)
     if retval != 0:
-        raise ValueError('finemapper command failed when running the following command:\n%s'%(cmd))
+        raise ValueError('finemapper command failed when running the following command:\n%s'%(finemapper_cmd))
     compare_dfs(tmpdir, gold_dir, outfile, sort_column='SNP')