[med-svn] [Git][med-team/python-pyfaidx][upstream] New upstream version 0.7.1

[Andreas Tille (@tille)]

Andreas Tille pushed to branch upstream at Debian Med / python-pyfaidx


Commits:
ef2f5ad8 by Andreas Tille at 2022-08-25T14:03:17+02:00
New upstream version 0.7.1
- - - - -


3 changed files:

- README.rst
- pyfaidx/__init__.py
- + tests/test_Path.py


Changes:

=====================================
README.rst
=====================================
@@ -26,7 +26,7 @@ If you use pyfaidx in your publication, please cite:
 Installation
 ------------
 
-This package is tested under Linux and macOS using Python 3.6+, and and is available from the PyPI:
+This package is tested under Linux and macOS using Python 3.7+, and and is available from the PyPI:
 
 ::
 
@@ -335,6 +335,17 @@ 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
+    
+    #new in v0.7.1
+    >>> from pyfaidx import Fasta
+    >>> from pathlib import Path
+    >>> genes = Fasta(Path('tests/data/genes.fasta'))
+    >>> genes
+    Fasta("tests/data/genes.fasta")
 
 Accessing fasta files from `filesystem_spec <https://filesystem-spec.readthedocs.io>`_ filesystems:
 


=====================================
pyfaidx/__init__.py
=====================================
@@ -353,7 +353,7 @@ class Faidx(object):
           Sequence() object or as a raw string.
           Default: False (i.e. return a Sequence() object).
         """
-        
+
         if fsspec and isinstance(filename, fsspec.core.OpenFile):
             self.filename = filename.path
             assert getattr(filename, 'mode', 'rb') == 'rb'
@@ -1061,7 +1061,6 @@ class Fasta(object):
         filename:  name of fasta file or fsspec.core.OpenFile instance
         indexname: name of index file or fsspec.core.OpenFile instance
         """
-        self.filename = filename
         self.mutable = mutable
         self.faidx = Faidx(
             filename,
@@ -1081,6 +1080,8 @@ class Fasta(object):
             rebuild=rebuild,
             build_index=build_index)
         
+        self.filename = self.faidx.filename
+        
         _record_constructor = MutableFastaRecord if self.mutable else FastaRecord
         self.records = OrderedDict([(rname, _record_constructor(rname, self)) for rname in self.faidx.index.keys()])
 
@@ -1175,10 +1176,6 @@ class FastaVariant(Fasta):
                  call_filter=None,
                  **kwargs):
         super(FastaVariant, self).__init__(filename, **kwargs)
-        try:
-            import pysam
-        except ImportError:
-            raise ImportError("pysam must be installed for FastaVariant.")
         try:
             import vcf
         except ImportError:


=====================================
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)
+
+ at 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



View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/ef2f5ad8f9d966e431c5f68625097c5c791bf1a6

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View it on GitLab: https://salsa.debian.org/med-team/python-pyfaidx/-/commit/ef2f5ad8f9d966e431c5f68625097c5c791bf1a6
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