From 880f6f95459e623c5167eda5b78179187bc9eacf Mon Sep 17 00:00:00 2001
From: Tobias Sargeant <tobiasjs@google.com>
Date: Tue, 28 Jul 2020 16:58:34 +0100
Subject: [PATCH 1/3] Fix Faidx.write_fai() to produce output readable by
 Faidx.read_fai()

* _index_as_string needs to be called.
* :n formats using the locale, bit int() doesn't parse using the locale,
  which means that numbers may be output with commas, and cannot be
  read back. Fix by formating with :d for this case.
---
 pyfaidx/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyfaidx/__init__.py b/pyfaidx/__init__.py
index d9f40f7..876a288 100644
--- a/pyfaidx/__init__.py
+++ b/pyfaidx/__init__.py
@@ -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.rlen:d}\t{v.offset:d}\t{v.lenc:d}\t{v.lenb:d}\n'.format(k=k, v=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):

From 19955ee0ea314c3e991336e460082d7f46a7372c Mon Sep 17 00:00:00 2001
From: Tobias Sargeant <tobiasjs@google.com>
Date: Tue, 28 Jul 2020 18:27:03 +0100
Subject: [PATCH 2/3] Add a test for Faidx.write_fai()

---
 tests/test_feature_indexing.py | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/tests/test_feature_indexing.py b/tests/test_feature_indexing.py
index e55dd9e..a0000aa 100644
--- a/tests/test_feature_indexing.py
+++ b/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.

From 956f315af48a22fe010a106eb53b5ea8b4db6604 Mon Sep 17 00:00:00 2001
From: Matt Shirley <mdshw5@gmail.com>
Date: Wed, 29 Jul 2020 10:22:21 -0400
Subject: [PATCH 3/3] Update IndexRecord.__str__ method to disregard locale

---
 pyfaidx/__init__.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyfaidx/__init__.py b/pyfaidx/__init__.py
index 876a288..0024904 100644
--- a/pyfaidx/__init__.py
+++ b/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 '{k}\t{v.rlen:d}\t{v.offset:d}\t{v.lenc:d}\t{v.lenb:d}\n'.format(k=k, v=v)
+          yield '{k}\t{v}\n'.format(k=k, v=str(v))
 
     def read_fai(self):
         try: