bionumpy - npm Package Compare versions

Comparing version 1.0.5 to 1.0.6

tests/conftest.py

+from pathlib import Path
+
+import pytest
+
+
[e-mail]()
+def data_path():
+    return Path(__file__).parent.parent / 'example_data'

bionumpy.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: bionumpy
-Version: 1.0.5
+Version: 1.0.6
 Summary: Library for working with biological sequence data as numpy arrays.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bionumpy/bionumpy

bionumpy.egg-info/SOURCES.txt

@@ -134,2 +134,3 @@ HISTORY.rst
 tests/buffers.py
+tests/conftest.py
 tests/fixtures.py
@@ -136,0 +137,0 @@ tests/genomic_fixtures.py

bionumpy/__init__.py

@@ -5,3 +5,3 @@ """Top-level package for bionumpy."""
 __email__ = "[e-mail]"
-__version__ = '1.0.5'
+__version__ = '1.0.6'
 
@@ -8,0 +8,0 @@ import npstructures as nps

bionumpy/io/indexed_fasta.py

@@ -0,1 +1,4 @@
+from pathlib import Path
+from typing import Union
+
 import numpy as np
@@ -64,5 +67,7 @@ from ..encoded_array import EncodedArray, as_encoded_array, EncodedRaggedArray
 
-    def __init__(self, filename: str):
+    def __init__(self, filename: Union[str, Path]):
+        if isinstance(filename, str):
+            filename = Path(filename)
         self._filename = filename
-        self._index = read_index(filename+".fai")
+        self._index = read_index(filename.with_suffix(filename.suffix + ".fai"))
         self._f_obj = open(filename, "rb")
@@ -69,0 +74,0 @@ self._index_table = FastaIdx.from_entry_tuples(

bionumpy/io/parser.py

 import codecs
 import logging
 import numpy as np
-from typing.io import IO
+try:
+    from typing import IO
+except ImportError:
+    from typing.io import IO
 from npstructures import npdataclass
@@ -6,0 +9,0 @@

PKG-INFO

 Metadata-Version: 2.1
 Name: bionumpy
-Version: 1.0.5
+Version: 1.0.6
 Summary: Library for working with biological sequence data as numpy arrays.
@@ -5,0 +5,0 @@ Home-page: https://github.com/bionumpy/bionumpy

setup.py

@@ -49,3 +49,3 @@ #!/usr/bin/env python
     url='https://github.com/bionumpy/bionumpy',
-    version='1.0.5',
+    version='1.0.6',
     zip_safe=False,
@@ -52,0 +52,0 @@ extras_require={'full': ['isal']}

tests/fixtures.py

@@ -6,12 +6,12 @@ from bionumpy import Bed6
     "bed": Bed6.from_entry_tuples([
-            ("chr1", 1, 3, ".", 0, "-"),
-            ("chr1", 40, 60, ".", 1, "+"),
-            ("chr20",  400, 600, ".", 2, "+")]),
+        ("chr1", 1, 3, ".", 0, "-"),
+        ("chr1", 40, 60, ".", 1, "+"),
+        ("chr20", 400, 600, ".", 2, "+")]),
     "vcf2": VCFEntry.from_entry_tuples([
-        ("chr1",	88361, "rs4970378",	"A",	"G", ".", ".", "."),
-        ("chr1",	887559, "rs3748595",	"A",	"CAA", ".", ".", "."),
-        ("chr2",	8877, "rs3828047",	"AGG",	"C", ".", ".", ".")]),
+        ("chr1", 88361, "rs4970378", "A", "G", ".", ".", "."),
+        ("chr1", 887559, "rs3748595", "A", "CAA", ".", ".", "."),
+        ("chr2", 8877, "rs3828047", "AGG", "C", ".", ".", ".")]),
     "fastq": SequenceEntryWithQuality.from_entry_tuples([
         ("headerishere", "CTTGTTGA", "".join("!" for _ in "CTTGTTGA")),
-        ("anotherheader", "CGG", "".join("~" for _ in "CGG"))]),}
+        ("anotherheader", "CGG", "".join("~" for _ in "CGG"))]), }
 '''
@@ -42,2 +42,4 @@ "vcf": [
         ('chr1',	9871,	9872,	0.17042)])
-}'''
+}'''
+
+

tests/io_tests/test_sam.py

@@ -80,8 +80,2 @@ import pytest
 
[e-mail]
-def tmp_path():
-    from pathlib import Path
-    path = Path('tmp_folder')
-    path.mkdir(exist_ok=True)
-    return path
 
@@ -103,4 +97,2 @@ @pytest.fixture
     d = f.read()
-    print(d)
-    print(d.flag.dtype)
     assert_encoded_array_equal(d.extra[-1], 'NM:i:1')
@@ -107,0 +99,0 @@

tests/test_bam.py

@@ -11,4 +11,5 @@ import numpy as np
 
-def test_read_acceptance():
-    filename = "example_data/test.bam"
+
+def test_read_acceptance(data_path):
+    filename = data_path / "test.bam"
     f = bnp.open(filename)
@@ -20,4 +21,4 @@ d = f.read()
 
-def test_read_intervals_acceptance():
-    filename = "example_data/test.bam"
+def test_read_intervals_acceptance(data_path):
+    filename = data_path / "test.bam"
     f = bnp.open(filename, buffer_type=BamIntervalBuffer)
@@ -30,4 +31,4 @@ d = f.read()
 @pytest.fixture()
-def bam_entries():
-    filename = get_file_name('example_data/small_alignments.bam')
+def bam_entries(data_path):
+    filename = data_path / 'small_alignments.bam'
     entries = bnp.open(filename).read()
@@ -52,8 +53,10 @@ return entries
 
-def test_write_bam(bam_entries):
+def test_write_bam(bam_entries, tmp_path):
     subset = bam_entries[bam_entries.mapq == 60]
-    with bnp.open('tmp.bam', mode='w') as f:
+
+    output_file = tmp_path / 'tmp.bam'
+    with bnp.open(output_file, mode='w') as f:
         f.write(subset)
-    assert open('tmp.bam', 'rb').read()[-28:] == b'\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00'
-    new_entries = bnp.open('tmp.bam').read()
+    assert open(output_file, 'rb').read()[-28:] == b'\x1f\x8b\x08\x04\x00\x00\x00\x00\x00\xff\x06\x00\x42\x43\x02\x00\x1b\x00\x03\x00\x00\x00\x00\x00\x00\x00\x00\x00'
+    new_entries = bnp.open(output_file).read()
     assert_array_equal(new_entries.position, subset.position)
@@ -60,0 +63,0 @@

tests/test_bnpdataclass.py

@@ -106,6 +106,7 @@ import dataclasses
 @pytest.mark.parametrize("file", [
-    "example_data/variants.vcf",
-    "example_data/variants_with_header.vcf"
+    "variants.vcf",
+    "variants_with_header.vcf"
 ])
-def test_read_header(file):
+def test_read_header(file,data_path):
+    file = data_path/file
     chunks = list(bnp.open(file).read_chunks())
@@ -112,0 +113,0 @@ true_header = "".join(line for line in open(file) if line.startswith("#"))

tests/test_encodedarrayfunctions.py

@@ -30,8 +30,8 @@ import pytest
 @pytest.fixture
-def intervals():
-    return bnp.open("example_data/ctcf.bed.gz").read()
+def intervals(data_path):
+    return bnp.open(data_path / "ctcf.bed.gz").read()
 
 @pytest.fixture
-def chrom_sizes():
-    return bnp.open("example_data/hg38.chrom.sizes").read()
+def chrom_sizes(data_path):
+    return bnp.open(data_path / "hg38.chrom.sizes").read()
 
@@ -38,0 +38,0 @@

tests/test_genomic_annotation.py

 from bionumpy.genomic_data import Genome
 
 
-def test_genomic_annotation():
-    g = Genome.from_file('example_data/hg38.chrom.sizes')
-    a = g.read_annotation('example_data/small_gff.gff3')
+def test_genomic_annotation(data_path):
+    g = Genome.from_file(data_path  / 'hg38.chrom.sizes')
+    a = g.read_annotation(data_path / 'small_gff.gff3')
     print(a.genes.gene_id)
     print(a.transcripts.transcript_id)
     print(a.exons.exon_id)

tests/test_groupby.py

@@ -68,4 +68,4 @@ import pytest
 #@pytest.mark.xfail
-def test_groupby_many_chunks():
-    file = "example_data/variants_with_header.vcf"
+def test_groupby_many_chunks(data_path):
+    file = data_path / "variants_with_header.vcf"
     chunks = bnp.open(file).read_chunks(100)
@@ -72,0 +72,0 @@ for chromosome, variants in bnp.groupby(chunks, "chromosome"):

tests/test_gtf.py

@@ -7,7 +7,6 @@ import pytest
 from bionumpy.util.testing import assert_encoded_array_equal
-from .util import get_file_name
 
 @pytest.fixture
-def gtf_entries():
-    return bnp.open(get_file_name("example_data/small.gtf")).read()
+def gtf_entries(data_path ):
+    return bnp.open(data_path / "small.gtf").read()
 
@@ -40,4 +39,4 @@ @pytest.fixture
 # @pytest.mark.skip('waiting')
-def test_read_gff():
-    annotation = bnp.open('example_data/small_gff.gff3').read()
+def test_read_gff(data_path):
+    annotation = bnp.open(data_path / 'small_gff.gff3').read()
     genes = annotation.get_genes()
@@ -49,5 +48,5 @@ assert genes[0].gene_id == 'ENSG00000290825.1'
 
-def test_read_sarcer_gtf():
-    annotation = bnp.open('example_data/sacCer3.ensGene.gtf.gz').read()
+def test_read_sarcer_gtf(data_path):
+    annotation = bnp.open(data_path / 'sacCer3.ensGene.gtf.gz').read()
     transcripts = annotation.get_transcripts()
     assert len(transcripts) > 0

tests/test_immuneml_compat.py

@@ -30,4 +30,4 @@ import dataclasses
 @pytest.fixture
-def file_name():
-    name = 'tmp1234.tsv'
+def file_name(tmp_path):
+    name = tmp_path / 'tmp1234.tsv'
     with open(name, 'w') as f:
@@ -38,4 +38,4 @@ f.write(text)
 @pytest.fixture
-def empty_file_name(header):
-    name = 'empty.csv'
+def empty_file_name(header, tmp_path):
+    name = tmp_path / 'empty.csv'
     with open(name, 'w') as f:
@@ -46,4 +46,4 @@ f.write(header)
 @pytest.fixture
-def full_file_name(full_text):
-    name = 'tmp1234full.tsv'
+def full_file_name(full_text, tmp_path):
+    name = tmp_path / 'tmp1234full.tsv'
     with open(name, 'w') as f:
@@ -50,0 +50,0 @@ f.write(full_text)

tests/test_indexed_fasta.py

@@ -18,9 +18,9 @@ from numpy.testing import assert_equal
 
-def test_fasta_index():
-    index = create_index("example_data/small_genome.fa")
+def test_fasta_index(data_path):
+    index = create_index(data_path / "small_genome.fa")
     assert_equal(index.length, [300, 600, 900, 1200])
 
 
-def test_dictlike():
-    idx_fasta = bnp.open_indexed("example_data/small_genome.fa")
+def test_dictlike(data_path):
+    idx_fasta = bnp.open_indexed(data_path / "small_genome.fa")
     assert list(idx_fasta.keys()) == ["0", "1", "2", "3"]
@@ -36,4 +36,4 @@ assert "Indexed Fasta" in repr(idx_fasta)
 
-def test_get_sequences():
-    idx_fasta = bnp.open_indexed("example_data/small_genome.fa")
+def test_get_sequences(data_path):
+    idx_fasta = bnp.open_indexed(data_path / "small_genome.fa")
     _intervals = Interval.from_entry_tuples([("1", 10, 20),
@@ -40,0 +40,0 @@ ("2", 11, 50),

tests/test_io.py

@@ -122,5 +122,4 @@ import os
 @pytest.mark.parametrize("buffer_name", ["bed", "vcf", "fastq", "fasta"])
-def test_ctx_manager_read(buffer_name):
-    file_path = Path(f"./{buffer_name}_example.{buffer_name}")
-
+def test_ctx_manager_read(buffer_name, tmp_path):
+    file_path = tmp_path / f"./{buffer_name}_example.{buffer_name}"
     with open(file_path, "w") as file:
@@ -132,5 +131,3 @@ file.write(buffer_texts[buffer_name])
 
-    os.remove(file_path)
 
-
 @pytest.mark.parametrize("buffer_name", ["bed", "vcf", "fastq", "fasta"])
@@ -170,6 +167,7 @@ def test_append_to_file(buffer_name):
 
-def test_write_empty():
+def test_write_empty(tmp_path):
     entry = VCFEntry([], [], [], [],
                      [], [], [], [])
-    with bnp.open('tmp.vcf', 'w') as f:
+    filename = tmp_path / 'tmp.vcf'
+    with bnp.open(filename, 'w') as f:
         f.write(entry)
@@ -198,3 +196,3 @@
 @pytest.fixture
-def fastq_with_carriage_return_filename():
+def fastq_with_carriage_return_filename(tmp_path):
     text = '''\
@@ -206,3 +204,3 @@ @test_sequence_id_here\r
 '''
-    filename = 'carriage_return.fq'
+    filename = tmp_path/'carriage_return.fq'
     with open(filename, 'w') as file:
@@ -214,3 +212,3 @@ file.write(text)
 @pytest.fixture
-def bed_with_carriage_return_filename():
+def bed_with_carriage_return_filename(tmp_path):
     text = '''\
@@ -220,3 +218,3 @@ chr1\t1\t2\r
 '''
-    filename = 'carriage_return.bed'
+    filename = tmp_path / 'carriage_return.bed'
     with open(filename, 'w') as file:
@@ -228,3 +226,3 @@ file.write(text)
 @pytest.fixture
-def fasta_with_carriage_return_filename():
+def fasta_with_carriage_return_filename(tmp_path):
     text = '''\
@@ -237,3 +235,3 @@ >test_sequence_id_here\r
 '''
-    filename = 'carriage_return.fa'
+    filename = tmp_path/'carriage_return.fa'
     with open(filename, 'w') as file:
@@ -264,13 +262,16 @@ file.write(text)
 # @pytest.mark.xfail
-def test_carriage_return_fai(fasta_with_carriage_return_filename):
+def test_carriage_return_fai(fasta_with_carriage_return_filename: Path):
     # remove file if it exists
-    if os.path.exists(fasta_with_carriage_return_filename + '.fai'):
-        os.remove(fasta_with_carriage_return_filename + '.fai')
-    fai = bnp.open_indexed(fasta_with_carriage_return_filename)
+    # add .fai to the end of the file
+    filename = fasta_with_carriage_return_filename
+    fai_filename = filename.with_suffix(filename.suffix + '.fai')
+    if os.path.exists(fai_filename):
+        os.remove(fai_filename)
+    fai = bnp.open_indexed(filename)
     assert_encoded_array_equal(fai['test_sequence_id_here'].raw(), 'GACTG')
     assert_encoded_array_equal(fai['test_sequence_id_here2'].raw(), 'GACTCGAG')
 
-def test_rwr_bed_with_change():
-    tmp_path = 'tmp_rwr.bed'
-    filename = get_file_name('example_data/alignments.bed')
+def test_rwr_bed_with_change(tmp_path, data_path):
+    file_path = tmp_path / 'tmp_rwr.bed'
+    filename = data_path  / 'alignments.bed'
     data = bnp.open(filename, buffer_type=bnp.io.Bed6Buffer).read()
@@ -281,10 +282,10 @@ data.start = data.start + 1
     data == data[::2]
-    if os.path.exists(tmp_path):
-        os.remove(tmp_path)
-    bnp.open(tmp_path, 'w', buffer_type=bnp.io.Bed6Buffer).write(data)
-    text = open(tmp_path).read()
+    if os.path.exists(file_path):
+        os.remove(file_path)
+    bnp.open(file_path, 'w', buffer_type=bnp.io.Bed6Buffer).write(data)
+    text = open(file_path).read()
     assert text.startswith('chr1'), text[:10]
     print(text)
-    data2 = bnp.open(tmp_path).read()
+    data2 = bnp.open(file_path).read()
     assert_equal(data.start, data2.start)
     assert np.all(data.chromosome == data2.chromosome)

tests/test_mutation_types.py

@@ -35,4 +35,4 @@ import pytest
 
-def test_cosmic_read():
-    matrix = bnp.io.read_matrix('example_data/COSMIC_v3.3.1_SBS_GRCh38.txt')
+def test_cosmic_read(data_path):
+    matrix = bnp.io.read_matrix(data_path / 'COSMIC_v3.3.1_SBS_GRCh38.txt')
     encoded = bnp.as_encoded_array(matrix.row_names.to_numpy_array(),
@@ -39,0 +39,0 @@ MutationTypeEncoding(1))

tests/test_parsers.py

@@ -58,13 +58,13 @@ import os
 
[e-mail]("file", ["example_data/reads.fq", "example_data/big.fq.gz"])
[e-mail]("file", ["reads.fq", "big.fq.gz"])
 @pytest.mark.parametrize("chunk_size", [100, 5000000])
-def test_buffered_writer_ctx_manager(file, chunk_size):
+def test_buffered_writer_ctx_manager(file, chunk_size, tmp_path, data_path):
+    file = data_path / file
+    file_path = tmp_path / "tmp.fq"
+    true_stream = bnp_open(data_path /'reads.fq').read_chunks()
 
-    file_path = "./tmp.fq"
-    true_stream = bnp_open('example_data/reads.fq').read_chunks()
-
     with bnp_open(file_path, mode='w') as f:
         f.write(true_stream)
 
-    true_stream = bnp_open('example_data/reads.fq').read_chunks()
+    true_stream = bnp_open(data_path / 'reads.fq').read_chunks()
     fq_stream = bnp_open(file_path)
@@ -74,3 +74,3 @@ for fq_item, true_item in zip(fq_stream, true_stream):
 
-    os.remove(file_path)
+    # os.remove(file_path)
 
@@ -118,3 +118,2 @@
 @pytest.mark.skip("makingtrouble")
[e-mail]("file_name", glob.glob("example_data/*"))
 def test_read_example_data(file_name):
@@ -189,4 +188,4 @@ if "broken" in file_name:
 
-def test_read_chunk_after_read_chunks_returns_empty_dataclass():
-    file = bnp.open("example_data/reads.fq")
+def test_read_chunk_after_read_chunks_returns_empty_dataclass(data_path):
+    file = bnp.open(data_path / 'reads.fq')
     chunks = list(file.read_chunks())
@@ -198,4 +197,4 @@ new_chunk = file.read_chunk()
 
-def test_read_gtf():
-    file = bnp.open("example_data/small.gtf")
+def test_read_gtf(data_path):
+    file = bnp.open(data_path / 'small.gtf')
     chunk = file.read_chunk()
@@ -205,5 +204,5 @@ assert True
 
-def test_read_bam():
-    data = bnp.open("example_data/alignments.bam").read()
-    data2 = bnp.open("example_data/alignments.sam").read()
+def test_read_bam(data_path):
+    data = bnp.open(data_path / 'alignments.bam').read()
+    data2 = bnp.open(data_path / 'alignments.sam').read()
     print(data)
@@ -216,4 +215,4 @@ print(data2)
     print(data)
-    n_lines = len([line for line in open("example_data/alignments.sam") if not line.startswith("@")])
+    n_lines = len([line for line in open(data_path / 'alignments.sam') if not line.startswith("@")])
     assert n_lines == len(data)
 

tests/test_position_weight_matrix.py

@@ -7,7 +7,7 @@ import pytest
 from bionumpy.io.jaspar import read_jaspar_matrix
-from bionumpy.sequence.position_weight_matrix import PositionWeightMatrix, _pwm_from_counts, PWM, get_motif_scores, get_motif_scores_old
-from bionumpy.encodings.alphabet_encoding import AlphabetEncoding
+from bionumpy.sequence.position_weight_matrix import PositionWeightMatrix, PWM, get_motif_scores, get_motif_scores_old
 from bionumpy import EncodedArray
 from bionumpy.io.motifs import read_motif
 
+
 @pytest.fixture
@@ -20,2 +20,3 @@ def neutral_ppm_dict():
 
+
 @pytest.fixture
@@ -58,3 +59,3 @@ def a_ppm_dict():
     log_prob = PositionWeightMatrix(pwm)(window)
-    np.testing.assert_allclose(np.exp(log_prob), 0.4*0.25)
+    np.testing.assert_allclose(np.exp(log_prob), 0.4 * 0.25)
 
@@ -65,22 +66,22 @@
     log_prob = PositionWeightMatrix(pwm).rolling_window(sequence)
-    np.testing.assert_allclose(np.exp(log_prob), [0.4*0.25, 0.025, 0.4*0.25])
+    np.testing.assert_allclose(np.exp(log_prob), [0.4 * 0.25, 0.025, 0.4 * 0.25])
 
 
-def test_integration():
+def test_integration(data_path):
     # Read the alphabet and counts from jaspar file
-    pwm = read_jaspar_matrix("example_data/MA0080.1.jaspar")
-    
+    pwm = read_jaspar_matrix(data_path /"MA0080.1.jaspar")
+
     # Convert counts to position weight matrix
     # pwm = PWM.from_dict(pwm)
-    
+
     # Make an array-class for the alphabet
     # encoding = AlphabetEncoding(alphabet)
-    
+
     # Get the motif score function
     # pwm = PWM(pwm, alphabet)
     motif_score = PositionWeightMatrix(pwm)
-    
-    #Get reads
-    entries = bnp.open("example_data/reads.fq").read()
-    
+
+    # Get reads
+    entries = bnp.open(data_path / "reads.fq").read()
+
     # Calculate the motif score for each valid window
@@ -90,5 +91,5 @@ scores = motif_score.rolling_window(entries.sequence)
 
-def test_read_csv_motif():
-    pwm = read_motif("example_data/pwm.csv")
-    pwm_jaspar = read_motif("example_data/pwm.jaspar")
+def test_read_csv_motif(data_path):
+    pwm = read_motif(data_path / "pwm.csv")
+    pwm_jaspar = read_motif(data_path / "pwm.jaspar")
     assert str(pwm) == str(pwm_jaspar)
@@ -99,5 +100,5 @@
     pwm = PWM(matrix, "ACGT")
-    #window = EncodedArray(window, AlphabetEncoding("ACGT"))
+    # window = EncodedArray(window, AlphabetEncoding("ACGT"))
     log_prob = pwm.calculate_score(window)
-    np.testing.assert_allclose(np.exp(log_prob), 0.4*0.25)
+    np.testing.assert_allclose(np.exp(log_prob), 0.4 * 0.25)
 
@@ -126,3 +127,3 @@
     scores = pwm.calculate_scores("AAC")
-    assert_array_equal(scores, [np.log(4**2), -np.inf, -np.inf])
+    assert_array_equal(scores, [np.log(4 ** 2), -np.inf, -np.inf])
 
@@ -136,3 +137,2 @@
     log_prob = pwm.calculate_score(window)
-    np.testing.assert_allclose(np.exp(log_prob), 0.4*0.25)
-    
+    np.testing.assert_allclose(np.exp(log_prob), 0.4 * 0.25)

tests/test_real_data.py

@@ -11,4 +11,4 @@ # Various tests for reading and parsing real data files
 
-def test_read_polaris_vcf():
-    data = bnp.open("example_data/polaris.vcf")
+def test_read_polaris_vcf(data_path):
+    data = bnp.open(data_path / "polaris.vcf")
 
@@ -20,10 +20,10 @@ for chunk in data:
 
-def test_read_syndip_vcf():
-    data = bnp.open("example_data/syndip.vcf").read()
+def test_read_syndip_vcf(data_path):
+    data = bnp.open(data_path / "syndip.vcf").read()
     print(data.info)
 
 
-def test_read_vcf_info_field_with_missing_header():
-    data = bnp.open("example_data/vcf_with_broken_header.vcf").read()
+def test_read_vcf_info_field_with_missing_header(data_path):
+    data = bnp.open(data_path / "vcf_with_broken_header.vcf").read()
     assert isinstance(data.info, EncodedRaggedArray) and data.info.encoding == bnp.BaseEncoding, \
         "Should parse as string when info tags missing"

tests/test_simulate.py

@@ -17,3 +17,2 @@ import pytest
 from numpy.random import default_rng
-from .util import get_file_name
 
@@ -110,4 +109,4 @@ rng = default_rng()
 
-def test_simulate_from_genome():
-    ref = get_file_name("example_data/small_genome.fa")
+def test_simulate_from_genome(data_path):
+    ref = data_path / "small_genome.fa"
     genome = bnp.Genome.from_file(ref)
@@ -125,4 +124,4 @@ genome = genome.read_sequence(ref)
 
-def test_simulate_variants():
-    ref = "example_data/small_genome.fa"
+def test_simulate_variants(data_path):
+    ref = data_path / "small_genome.fa"
     genome = bnp.Genome.from_file(ref)
@@ -129,0 +128,0 @@ genome = genome.read_sequence(ref)

tests/test_string_array.py

@@ -36,4 +36,4 @@ import numpy as np
 @pytest.fixture
-def file_name():
-    name = 'string_array_test.txt'
+def file_name(tmp_path):
+    name = tmp_path / 'string_array_test.txt'
     open(name, 'w').write(
@@ -40,0 +40,0 @@ '''\

tests/test_string_encodings.py

@@ -27,4 +27,4 @@ import pytest
 @pytest.fixture
-def chrom_names():
-    return bnp.open("example_data/hg38.chrom.sizes").read().name
+def chrom_names(data_path):
+    return bnp.open(data_path / "hg38.chrom.sizes").read().name
 
@@ -31,0 +31,0 @@

tests/test_strops.py

@@ -114,5 +114,5 @@ import pytest
 
-def test_chromosome_str_equal():
-    bam = bnp.open("example_data/test.bam").read()
-    bam2 = bnp.open("example_data/test.bam").read()
+def test_chromosome_str_equal(data_path):
+    bam = bnp.open(data_path / "test.bam").read()
+    bam2 = bnp.open(data_path / "test.bam").read()
     assert np.all(str_equal(bam.chromosome, bam2.chromosome))
@@ -119,0 +119,0 @@

tests/test_vcf_encoding.py

 import dataclasses
-import bionumpy as bnp
 import numpy as np
 from npstructures.testing import assert_raggedarray_equal
 from numpy.testing import assert_array_equal
-from bionumpy.bnpdataclass import BNPDataClass
 import bionumpy as bnp
@@ -14,13 +12,13 @@ import bionumpy.encoded_array
 
-from bionumpy.datatypes import VCFEntry, VCFEntryWithGenotypes
+from bionumpy.datatypes import VCFEntryWithGenotypes
 from bionumpy.encodings.vcf_encoding import PhasedGenotypeRowEncoding, GenotypeRowEncoding, PhasedHaplotypeRowEncoding
 from bionumpy.util.testing import assert_bnpdataclass_equal
-from tests.util import get_file_name
 
 
-def test_vcf_matrix_buffer():
-    f = bnp.open("example_data/variants_with_header.vcf",
+def test_vcf_matrix_buffer(tmp_path, data_path):
+    f = bnp.open(data_path / "variants_with_header.vcf",
                  buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
 
-    out = bnp.open("test1.vcf", mode="w")
+    out_path = tmp_path / "test1.vcf"
+    out = bnp.open(out_path, mode="w")
 
@@ -32,23 +30,24 @@ for chunk in f:
 
-    filestart = open('test1.vcf').read(100)
+    filestart = open(out_path).read(100)
     assert filestart.startswith('#'), filestart
     # check that header was written
-    chunk = bnp.open("test1.vcf").read_chunk()
+    chunk = bnp.open(out_path).read_chunk()
     assert chunk.get_context("header") != "" and chunk.get_context("header") == header
 
 
-def test_vcf_matrix_buffer_stream():
-    f = bnp.open("example_data/variants_with_header.vcf",
+def test_vcf_matrix_buffer_stream(tmp_path, data_path):
+    f = bnp.open(data_path / "variants_with_header.vcf",
                  buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
 
-    out = bnp.open("test1.vcf", mode="w")
+    outpath = tmp_path / "test1.vcf"
+    out = bnp.open(outpath, mode="w")
     out.write(f.read_chunks())
     # check that header was written
-    chunk = bnp.open("test1.vcf").read_chunk()
+    chunk = bnp.open(outpath).read_chunk()
     assert chunk.get_context("header") != ""
 
-def test_context_state():
-    f = bnp.open("example_data/variants_with_header.vcf").read()
+def test_context_state(data_path):
+    f = bnp.open(data_path / "variants_with_header.vcf").read()
     assert f.get_context("header")
-    f2 = bnp.open("example_data/variants.vcf").read()
+    f2 = bnp.open(data_path / "variants.vcf").read()
     assert not f2.get_context("header")
@@ -101,5 +100,5 @@
 
-def test_parse_unphased_vcf():
-    # example_data/variants.vcf has messy unphased and missing genotypes
-    filename = "example_data/variants.vcf"
+def test_parse_unphased_vcf(data_path):
+    # variants.vcf has messy unphased and missing genotypes
+    filename = data_path / "variants.vcf"
     print(open(filename).read())
@@ -125,4 +124,4 @@ f = bnp.open(filename, buffer_type=bionumpy.io.vcf_buffers.VCFMatrixBuffer)
 
-def test_parse_phased_vcf():
-    f = bnp.open("example_data/variants_phased.vcf", buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
+def test_parse_phased_vcf(data_path):
+    f = bnp.open(data_path / "variants_phased.vcf", buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
     data = f.read()
@@ -139,4 +138,4 @@ data = data.genotypes.raw()
 
-def test_read_info_field():
-    vcf_filename = "example_data/variants_with_header.vcf"
+def test_read_info_field(data_path):
+    vcf_filename = data_path / "variants_with_header.vcf"
     f = bnp.open(vcf_filename,
@@ -152,4 +151,4 @@ buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
 @pytest.mark.skip('missing data')
-def test_read_info_field2():
-    vcf_filename = "example_data/info_flag.vcf"
+def test_read_info_field2(data_path):
+    vcf_filename = data_path / "info_flag.vcf"
     f = bnp.open(vcf_filename,
@@ -163,4 +162,4 @@ buffer_type=bionumpy.io.vcf_buffers.PhasedVCFMatrixBuffer)
 # @pytest.mark.xfail
-def test_read_biallelic_vcf():
-    file_name = "example_data/small_phased_biallelic.vcf"
+def test_read_biallelic_vcf(data_path):
+    file_name = data_path / "small_phased_biallelic.vcf"
     vcf = bnp.open(file_name, buffer_type=bnp.io.vcf_buffers.PhasedHaplotypeVCFMatrixBuffer)
@@ -172,4 +171,4 @@ for chunk in vcf.read_chunks():
 @pytest.mark.xfail
-def test_read_info_from_vcf():
-    file = "example_data/variants_with_single_individual_genotypes_and_info.vcf"
+def test_read_info_from_vcf(data_path):
+    file = data_path / "variants_with_single_individual_genotypes_and_info.vcf"
     variants = bnp.open(file).read()
@@ -183,4 +182,4 @@
 @pytest.mark.skip
-def test_concatenate_variants():
-    file = "example_data/variants_with_single_individual_genotypes_and_info.vcf"
+def test_concatenate_variants(data_path):
+    file = data_path / "variants_with_single_individual_genotypes_and_info.vcf"
     f = bnp.open(file)
@@ -210,4 +209,4 @@ chunk1 = f.read_chunk(min_chunk_size=200)
 @pytest.fixture
-def data_with_info():
-    file = "example_data/vcf_symbolic_sequences.vcf"
+def data_with_info(data_path):
+    file = data_path / "vcf_symbolic_sequences.vcf"
     data = bnp.open(file).read()
@@ -246,4 +245,4 @@ return data
 # @pytest.mark.skip  # .genotype not implemented
-def test_read_genotype_data_from_messy_vcf():
-    file_name = "example_data/polaris_small.vcf"
+def test_read_genotype_data_from_messy_vcf(data_path):
+    file_name = data_path / "polaris_small.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -254,4 +253,4 @@ genotype = data.genotype[0]
 
-def test_read_genotype_with_more_data():
-    file_name = get_file_name("example_data/syndip.vcf")
+def test_read_genotype_with_more_data(data_path):
+    file_name = data_path / "syndip.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -261,3 +260,3 @@ genotypes = data.genotype[:4]
 
-def test_write_genotype():
+def test_write_genotype(tmp_path):
     data = narrow_type(VCFEntryWithGenotypes, 'info', str)(
@@ -274,9 +273,10 @@ ['chr1', 'chr2'],
     )
-    with bnp.open("tmp.vcf", "w", buffer_type=VCFBuffer2) as f:
+    file_path = tmp_path / "tmp.vcf"
+    with bnp.open(file_path, "w", buffer_type=VCFBuffer2) as f:
         f.write(data)
-    new_data = bnp.open("tmp.vcf", buffer_type=VCFBuffer2).read().get_data_object()
+    new_data = bnp.open(file_path, buffer_type=VCFBuffer2).read().get_data_object()
     assert_bnpdataclass_equal(data, new_data)
 
-def test_read_genotype_with_no_data():
-    file_name = "example_data/variants_without_genotypes.vcf"
+def test_read_genotype_with_no_data(data_path):
+    file_name = data_path / "variants_without_genotypes.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -286,4 +286,4 @@ genotypes = data.genotype[:4]
 
-def test_read_empty_vcf():
-    file_name = get_file_name("example_data/empty_variants.vcf")
+def test_read_empty_vcf(data_path):
+    file_name = data_path / "empty_variants.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -294,4 +294,4 @@ assert len(data) == 0
 @pytest.mark.skip   # genotype fields not implemented
-def test_read_genotype_ad_field():
-    file_name = "example_data/syndip.vcf"
+def test_read_genotype_ad_field(data_path):
+    file_name = data_path / "syndip.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -305,4 +305,4 @@ assert_array_equal(data[0].genotype_data.AD == [1, 1])
 @pytest.mark.skip   # genotype fields not implemented
-def test_read_genotype_ad_field():
-    file_name = "example_data/syndip.vcf"
+def test_read_genotype_ad_field(data_path):
+    file_name = data_path / "syndip.vcf"
     data = bnp.open(file_name, buffer_type=VCFBuffer2).read()
@@ -315,4 +315,4 @@ assert_array_equal(data[0].genotype_data.AD == [1, 1])
 
-def test_read_thousand_genomes_info_field():
-    data = bnp.open("example_data/thousand_genomes.vcf").read()
+def test_read_thousand_genomes_info_field(data_path):
+    data = bnp.open(data_path / "thousand_genomes.vcf").read()
 
@@ -327,4 +327,4 @@ assert_raggedarray_equal(
 
-def test_read_hprc_multiallelic():
-    data = bnp.open(get_file_name("example_data/hprc_multiallelic.vcf")).read()
+def test_read_hprc_multiallelic(data_path):
+    data = bnp.open(data_path / "hprc_multiallelic.vcf").read()
     result = data.info.AF[0:2]
@@ -337,4 +337,4 @@ assert_raggedarray_equal(result, [
 
-def test_read_write_vcf_gives_identical_file():
-    file = "example_data/variants_with_single_individual_genotypes_and_info.vcf"
+def test_read_write_vcf_gives_identical_file(data_path):
+    file = data_path /"variants_with_single_individual_genotypes_and_info.vcf"
     variants = bnp.open(file).read()
@@ -353,3 +353,3 @@
 def test_read_vcf_replace_field():
-    file = "example_data/variants_with_single_individual_genotypes_and_info.vcf"
+    file = data_path / "variants_with_single_individual_genotypes_and_info.vcf"
     variants = bnp.open(file).read()
@@ -370,15 +370,15 @@ variants = bnp.replace(variants, position=np.ones_like(variants.position))
 #@pytest.mark.xfail
-def test_parse_vcf_that_fails():
-    vcf = bnp.open(get_file_name("example_data/variants_with_af.vcf")).read()
+def test_parse_vcf_that_fails(data_path):
+    vcf = bnp.open(data_path /"variants_with_af.vcf").read()
     print(vcf)
 
 
-def test_genotype_print():
-    i = bnp.open(get_file_name("example_data/thousand_genomes.vcf"),
+def test_genotype_print(data_path):
+    i = bnp.open(data_path / "thousand_genomes.vcf",
                  buffer_type=VCFBuffer2).read()
     print(i.genotype)
 
-def test_ioi():
-    out_filename = "tmp_ioi.vcf"
-    i = bnp.open(get_file_name("example_data/thousand_genomes.vcf"),
+def test_ioi(tmp_path, data_path):
+    out_filename = tmp_path / "tmp_ioi.vcf"
+    i = bnp.open(data_path / "thousand_genomes.vcf",
                  buffer_type=VCFBuffer2).read()
@@ -393,4 +393,4 @@ print(i.genotype)
 
-def test_vcf_haplotyped():
-    vcf = bnp.open(get_file_name("example_data/haplotypes.vcf"), buffer_type=VCFHaplotypeBuffer).read()
+def test_vcf_haplotyped(data_path ):
+    vcf = bnp.open(data_path / "haplotypes.vcf", buffer_type=VCFHaplotypeBuffer).read()
     print(vcf.genotype)
@@ -397,0 +397,0 @@ genotype_ = vcf.genotype[1][:3]

tests/test_vcf.py

@@ -0,5 +1,7 @@
+import os
+
 from bionumpy.io.vcf_header import parse_header
 import bionumpy as bnp
 import pytest
-
+from .conftest import data_path
 from bionumpy.util.testing import assert_encoded_array_equal
@@ -95,4 +97,4 @@
 
-def test_vcf_lof():
-    variants = bnp.open("example_data/lof_file.vcf").read()
+def test_vcf_lof(data_path):
+    variants = bnp.open(data_path / "lof_file.vcf").read()
     lof = variants.info.LoF
@@ -107,4 +109,4 @@ n_variants = len(variants)
 
-def test_vcf_info_data_object():
-    variants = bnp.open("example_data/lof_file.vcf").read()
+def test_vcf_info_data_object(data_path):
+    variants = bnp.open(data_path / "lof_file.vcf").read()
     info = variants.info.get_data_object()
@@ -114,14 +116,18 @@ print(str(info))
 
-def test_vcf_filtering_chunk():
-    with bnp.open('tmp.vcf', 'w') as f:
-        for chunk in bnp.open("example_data/lof_file.vcf").read_chunks():
+
+def test_vcf_filtering_chunk(tmp_path, data_path):
+    in_filepath = data_path / "lof_file.vcf"
+    out_filepath = tmp_path / 'tmp.vcf'
+    with bnp.open(out_filepath, 'w') as f:
+        for chunk in bnp.open(in_filepath).read_chunks():
             f.write(chunk[(chunk.info.LoF.lengths > 0) & chunk.info.ONCOGENE])
-    assert bnp.count_entries('tmp.vcf') == 2
+    assert bnp.count_entries(out_filepath) == 2
 
 
-def test_locations():
+def test_locations(data_path):
     k = 5
     # Read genome and variants
-    genome = bnp.Genome.from_file("example_data/sacCer3.fa", filter_function=None)
-    variants_file = "example_data/sacCer3_sample_variants.vcf.gz"
+    genome_file_name = data_path / "sacCer3.fa"
+    genome = bnp.Genome.from_file(genome_file_name, filter_function=None)
+    variants_file = data_path / "sacCer3_sample_variants.vcf.gz"
     print(bnp.open(variants_file).read())
@@ -137,3 +143,3 @@
     print(variants)
-    windows = variants.get_windows(flank=k-1)
+    windows = variants.get_windows(flank=k - 1)
     print(windows)
@@ -146,3 +152,3 @@ # Use the windows to extract sequences (kmers)
     assert_encoded_array_equal(sequences[:, k - 1], variants.get_data_field('ref_seq').ravel())
-    sequences[:, k-1] = variants.get_data_field('alt_seq').ravel()
+    sequences[:, k - 1] = variants.get_data_field('alt_seq').ravel()
     assert_encoded_array_equal(sequences[:, k - 1], variants.get_data_field('alt_seq').ravel())
@@ -152,2 +158,6 @@ print(sequences)
     alt_kmers = bnp.get_kmers(sequences, k)
-    print(alt_kmers[0:3])
+    print(alt_kmers[0:3])
+    fai_filename = genome_file_name.with_suffix(genome_file_name.suffix + '.fai')
+    # remove file
+    if os.path.exists(fai_filename):
+        os.remove(fai_filename)

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