Merge pull request #166 from folded/fix_write_fai

Fix write_fai

pyfaidx/__init__.py

@@ -305,7 +305,7 @@ def __getitem__(self, key):
         return tuple.__getitem__(self, key)
 
     def __str__(self):
-        return "{rlen:n}\t{offset:n}\t{lenc:n}\t{lenb:n}\n".format(
+        return "{rlen:d}\t{offset:d}\t{lenc:d}\t{lenb:d}".format(
             **self._asdict())
 
     def __len__(self):
@@ -460,7 +460,7 @@ def __repr__(self):
     def _index_as_string(self):
         """ Returns the string representation of the index as iterable """
         for k, v in self.index.items():
-            yield '\t'.join([k, str(v)])
+          yield '{k}\t{v}\n'.format(k=k, v=str(v))
 
     def read_fai(self):
         try:
@@ -607,7 +607,7 @@ def build_index(self):
     def write_fai(self):
         with self.lock:
             with open(self.indexname, 'w') as outfile:
-                for line in self._index_as_string:
+                for line in self._index_as_string():
                     outfile.write(line)
 
     def from_buffer(self, start, end):

tests/test_feature_indexing.py

@@ -317,12 +317,24 @@ def test_open(*args, **kwargs):
         finally:
             shutil.rmtree(tmp_dir)
 
+    def test_read_back_index(self):
+        """Ensure that index files written with write_fai() can be read back"""
+        import locale
+        old_locale = locale.getlocale(locale.LC_NUMERIC)
+        try:
+            locale.setlocale(locale.LC_NUMERIC, 'en_US.utf8')
+            faidx = Faidx('data/genes.fasta')
+            faidx.write_fai()
+            faidx = Faidx('data/genes.fasta', build_index=False)
+        finally:
+            locale.setlocale(locale.LC_NUMERIC, old_locale)
+
     @raises(IndexNotFoundError)
     def test_issue_134_no_build_index(self):
         """ Ensure that index file is not built when build_index=False. See mdshw5/pyfaidx#134.
         """
         faidx = Faidx('data/genes.fasta', build_index=False)
-        
+
     @raises(FastaIndexingError)
     def test_issue_144_no_defline(self):
         """ Ensure that an exception is raised when a file contains no deflines. See mdshw5/pyfaidx#144.