fix the SyntaxWarning

JianYang-Lab · Dec 9, 2024 · 5dfe4cf · 5dfe4cf
1 parent f98a45d
commit 5dfe4cf
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Showing 4 changed files with 10 additions and 16 deletions.
diff --git a/src/gsMap/diagnosis.py b/src/gsMap/diagnosis.py
@@ -9,7 +9,7 @@
 
 from gsMap.config import DiagnosisConfig
 from gsMap.utils.manhattan_plot import ManhattanPlot
-from gsMap.visualize import draw_scatter, load_st_coord, estimate_point_size_for_plot
+from gsMap.visualize import draw_scatter, load_st_coord, estimate_point_size_for_plot,load_ldsc
 
 
 warnings.filterwarnings("ignore", category=FutureWarning)
@@ -23,16 +23,6 @@ def convert_z_to_p(gwas_data):
     gwas_data['P'] = gwas_data['P'].clip(lower=min_p_value)
     return gwas_data
 
-
-def load_ldsc(ldsc_input_file):
-    """Load LDSC data and calculate logp."""
-    ldsc = pd.read_csv(ldsc_input_file, compression='gzip')
-    ldsc['spot'] = ldsc['spot'].astype(str).replace('\.0', '', regex=True)
-    ldsc.set_index('spot', inplace=True)
-    ldsc['logp'] = -np.log10(ldsc['p'])
-    return ldsc
-
-
 def load_gene_diagnostic_info(config:DiagnosisConfig):
     """Load or compute gene diagnostic info."""
     gene_diagnostic_info_save_path = config.get_gene_diagnostic_info_save_path(config.trait_name)

diff --git a/src/gsMap/utils/generate_r2_matrix.py b/src/gsMap/utils/generate_r2_matrix.py
@@ -69,7 +69,7 @@ def read(self, fname):
                 raise ValueError('{f} filename must end in {f}'.format(f=end))
             comp = get_compression(fname)
             self.df = pd.read_csv(fname, header=self.header, usecols=self.usecols,
-                                  sep='\s+', compression=comp)
+                                  sep=r'\s+', compression=comp)
             if self.colnames:
                 self.df.columns = self.colnames
             if self.keepcol is not None:

diff --git a/src/gsMap/utils/regression_read.py b/src/gsMap/utils/regression_read.py
@@ -60,7 +60,7 @@ def read_csv(fh, **kwargs):
     '''
     Read the csv data
     '''
-    return pd.read_csv(fh, sep='\s+', na_values='.', **kwargs)
+    return pd.read_csv(fh, sep=r'\s+', na_values='.', **kwargs)
 
 
 # Fun for reading loading LD scores 

diff --git a/src/gsMap/visualize.py b/src/gsMap/visualize.py
@@ -11,9 +11,13 @@
 
 
 def load_ldsc(ldsc_input_file):
-    ldsc = pd.read_csv(ldsc_input_file, compression='gzip')
-    ldsc.spot = ldsc.spot.astype(str).replace('\.0', '', regex=True)
-    ldsc.index = ldsc.spot
+    ldsc = pd.read_csv(
+            ldsc_input_file,
+            compression='gzip',
+            dtype={'spot': str, 'p': float},
+            index_col='spot',
+            usecols=['spot', 'p']
+        )
     ldsc['logp'] = -np.log10(ldsc.p)
     return ldsc