Merge pull request mdshw5#184 from palao/develop

pathlib.Path can be passed to Fasta and Faidx
eroller · Jan 31, 2022 · 18993f7 · 18993f7
2 parents 5a81446 + bdb6d7a
commit 18993f7
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diff --git a/.gitignore b/.gitignore
@@ -10,3 +10,6 @@ __pycache__
 .coverage
 .coverage.*
 tests/data/chr22*
+.eggs/
+tests/data/genes.fasta.gz
+*~
diff --git a/README.rst b/README.rst
@@ -335,6 +335,16 @@ The FastaVariant class provides a way to integrate single nucleotide variant cal
     >>> consensus = FastaVariant('tests/data/chr22.fasta', 'tests/data/chr22.vcf.gz', sample='NA06984', het=True, hom=True, call_filter='GT == "0/1"')
     >>> consensus['22'].variant_sites
     (16042793, 29187373, 29187448, 29194610, 29821332)
+    
+You can also specify paths using ``pathlib.Path`` objects.
+
+.. code:: python
+
+    >>> from pyfaidx import Fasta
+    >>> from pathlib import Path
+    >>> genes = Fasta(Path('tests/data/genes.fasta'))
+    >>> genes
+    Fasta("tests/data/genes.fasta")
 
 .. _faidx:
 

diff --git a/pyfaidx/__init__.py b/pyfaidx/__init__.py
@@ -344,6 +344,7 @@ def __init__(self,
           Sequence() object or as a raw string.
           Default: False (i.e. return a Sequence() object).
         """
+        filename = str(filename)
         self.filename = filename
 
         if filename.lower().endswith('.bgz') or filename.lower().endswith(
@@ -997,6 +998,7 @@ def __init__(self,
         An object that provides a pygr compatible interface.
         filename: name of fasta file
         """
+        filename = str(filename)
         self.filename = filename
         self.mutable = mutable
         self.faidx = Faidx(

diff --git a/tests/test_Path.py b/tests/test_Path.py
@@ -0,0 +1,29 @@
+import os
+import pytest
+from pathlib import Path
+from pyfaidx import Faidx, Fasta
+
+path = os.path.dirname(__file__)
+os.chdir(path)
+
+@pytest.fixture
+def remove_index():
+    yield
+    try:
+        os.remove('data/genes.fasta.fai')
+    except EnvironmentError:
+        pass  # some tests may delete this file
+
+def test_Faidx(remove_index):
+    """ Ensures that Faidx can be created with a pathlib.Path as filename """
+    filename = 'data/genes.fasta'
+    faidx = Faidx(filename)
+    faidx_w_path = Faidx(Path(filename))
+    assert faidx.filename == faidx_w_path.filename
+
+def test_Fasta(remove_index):
+    """ Ensures that Fasta can be created with a pathlib.Path as filename """
+    filename = 'data/genes.fasta'
+    fasta = Fasta(filename)
+    fasta_w_path = Fasta(Path(filename))
+    assert fasta.filename == fasta_w_path.filename