Fix Path handling issues in VCFWriter, BEDWriter and PGENWriter

AI-sandbox · Nov 15, 2024 · 392fef9 · 392fef9
1 parent bdd8758
commit 392fef9
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/snputils/snp/io/write/bed.py b/snputils/snp/io/write/bed.py
@@ -27,7 +27,7 @@ def write(self):
 
         # Save .bed file
         if self.__filename.suffix != '.bed':
-            self.__filename = self.__filename.with_name(self.__filename.name + '.bed')
+            self.__filename = self.__filename.with_name(self.__filename.with_suffix('.bed'))
 
         log.info(f"Writing .bed file: {self.__filename}")
 
@@ -40,7 +40,7 @@ def write(self):
         samples, variants = self.__snpobj.calldata_gt.shape
 
         # Define the PgenWriter to save the data
-        data_save = pg.PgenWriter(filename=self.__filename.encode('utf-8'),
+        data_save = pg.PgenWriter(filename=str(self.__filename).encode('utf-8'),
                                   sample_ct=samples,
                                   variant_ct=variants,
                                   nonref_flags=True,
@@ -70,7 +70,7 @@ def write(self):
         fam_file['fid'] = self.__snpobj.samples
 
         # Save .fam file
-        fam_file.to_csv(self.__filename + '.fam', sep='\t', index=False, header=False)
+        fam_file.to_csv(self.__filename.with_suffix('.fam'), sep='\t', index=False, header=False)
         log.info(f"Finished writing .fam file: {self.__filename}")
 
         # Save .bim file
@@ -87,5 +87,5 @@ def write(self):
         bim_file['a1'] = self.__snpobj.variants_ref
 
         # Save .bim file
-        bim_file.to_csv(self.__filename + '.bim', sep='\t', index=False, header=False)
+        bim_file.to_csv(self.__filename.with_suffix('.bim'), sep='\t', index=False, header=False)
         log.info(f"Finished writing .bim file: {self.__filename}")
diff --git a/snputils/snp/io/write/pgen.py b/snputils/snp/io/write/pgen.py
@@ -92,7 +92,7 @@ def write_pgen(self):
             flat_genotypes = self.__snpobj.__calldata_gt
 
         with pg.PgenWriter(
-            f"{self.__filename}.pgen".encode("utf-8"),
+            filename=str(self.__filename).encode('utf-8'),
             sample_ct=num_samples,
             variant_ct=num_variants,
             hardcall_phase_present=phased,

diff --git a/snputils/snp/io/write/vcf.py b/snputils/snp/io/write/vcf.py
@@ -104,9 +104,9 @@ def write_chromosome_data(self, chrom, data_chrom):
 
         # Format output file
         if chrom == "All":
-            file = self.__filename + self.__file_extension
+            file = self.__filename.with_suffix(self.__file_extension)
         else:
-            file = f'{self.__filename}_{chrom}{self.__file_extension}'
+            file = self.__filename.parent / f"{self.__filename.stem}_{chrom}{self.__file_extension}"
 
         # Write header
         with open(file, "w") as f: