.

granite/lib/vcf_parser.py

@@ -294,7 +294,8 @@ def get_genotype_value(self, ID_genotype, tag_to_get, sep=':'):
 
     @staticmethod
     def read_vcf(inputfile):
-        ''' generator that reads vcf file, gzipped or ungzipped '''
+        ''' read vcf file, gzipped or ungzipped,
+        return a generator '''
         if inputfile.endswith('.gz'):
             with gzip.open(inputfile, 'rb') as fz:
                 for byteline in fz:
@@ -352,49 +353,24 @@ def parse_variants(self): # generator
     #end def
 
     def write_definitions(self, outputfile_obj):
-        ''' write header definitions to file.
-
-        ::
-             with open(somefilename, 'w') as fo:
-                 vcf_obj.write_definitions(fo)
-
-        '''
+        ''' write header definitions to outputfile_obj buffer '''
         outputfile_obj.write(self.header.definitions)
     #end def
 
     def write_columns(self, outputfile_obj):
-        ''' write header columns to file,
-        #CHROM ...
-
-        ::
-             with open(somefilename, 'w') as fo:
-                 vcf_obj.write_columns(fo)
-
-        '''
+        ''' write header columns to outputfile_obj buffer,
+        #CHROM ... '''
         outputfile_obj.write(self.header.columns)
     #end def
 
     def write_header(self, outputfile_obj):
-        ''' write header definitions and columns to file.
-
-        ::
-             with open(somefilename, 'w') as fo:
-                 vcf_obj.write_header(fo)
-
-        '''
+        ''' write header definitions and columns to outputfile_obj buffer '''
         self.write_definitions(outputfile_obj)
         self.write_columns(outputfile_obj)
     #end def
 
     def write_variant(self, outputfile_obj, parsed_variant):
-        ''' write parsed_variant (Variant object generated by parse_variants) to file.
-
-        ::
-             with open(somefilename, 'w') as fo:
-                 for vnt_obj in vcf_obj.parse_variants():
-                     vcf_obj.write_variant(fo, vnt_obj)
-
-        '''
+        ''' write parsed_variant (Variant object generated by parse_variants) to outputfile_obj buffer '''
         outputfile_obj.write(parsed_variant.to_string())
     #end def
 

tests/test_vcf_parser.py

@@ -75,6 +75,7 @@ def test_read_vcf():
     vcflines = vcf_parser.Vcf.read_vcf('tests/files/input_vcf_parser.vcf')
     assert next(vcflines) == '##fileformat=VCFv4.1\n'
     assert next(vcflines) == '##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location">\n'
+#end def
 
 def test_read_vcf_gz():
     ''' '''
@@ -84,21 +85,25 @@ def test_read_vcf_gz():
     assert next(vcflines) == next(vcflines_gz)
     assert next(vcflines) == next(vcflines_gz)
     assert next(vcflines) == next(vcflines_gz)
+#end def
 
 def test_write_header():
     ''' '''
     # Creating Vcf object
     vcf_obj = vcf_parser.Vcf('tests/files/input_vcf_parser.vcf')
-    # write
+    # Write
     with open('tests/files/test_write_header.out', 'w') as fo:
         vcf_obj.write_definitions(fo)
-    # test
+    #end with
+    # Test
     with open('tests/files/test_write_header.out', 'r') as f:
         output_headers = f.read()
+    #end with
     input_headers = vcf_obj.header.definitions
     assert output_headers == input_headers
-    # clean up
+    # Clean up
     os.remove('tests/files/test_write_header.out')
+#end def
 
 def test_write_variant():
     ''' '''
@@ -108,10 +113,15 @@ def test_write_variant():
     with open('tests/files/test_write_variants.out', 'w') as fo:
         for rec in vcf_obj.parse_variants():
             vcf_obj.write_variant(fo, rec)
-    # test
+        #end for
+    #end with
+    # Test
     recs = vcf_obj.parse_variants()
     with open('tests/files/test_write_variants.out', 'r') as f:
         for line in f:
             assert line == next(recs).to_string()
-    # clean up
+        #end for
+    #end with
+    # Clean up
     os.remove('tests/files/test_write_variants.out')
+#end def