DEV: finish unit tests

beardymcjohnface · Jun 22, 2023 · c6a2969 · c6a2969
1 parent aa5ddbe
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diff --git a/README.md b/README.md
@@ -2,6 +2,7 @@
 
 [![](https://img.shields.io/static/v1?label=Licence&message=MIT&color=black)](https://opensource.org/license/mit/)
 [![install with PyPI](https://img.shields.io/badge/Install%20with-PyPI-brightgreen.svg?style=flat-square)](https://pypi.org/project/metasnek/)
+[![codecov](https://codecov.io/gh/beardymcjohnface/metasnek/branch/main/graph/badge.svg?token=lCyqJhuiCN)](https://codecov.io/gh/beardymcjohnface/metasnek)
 
 Misc functions for metagenomic pipelines
 

diff --git a/tests/test_fastq_finder.py b/tests/test_fastq_finder.py
@@ -2,7 +2,7 @@
 import warnings
 import pytest
 import shutil
-from metasnek.fastq_finder import parse_directory, parse_tsv_file, parse_samples
+from metasnek.fastq_finder import parse_directory, parse_tsv_file, parse_samples, convert_to_dictionary, parse_samples_to_dictionary, write_samples_tsv
 
 
 @pytest.fixture(scope="session")
@@ -145,3 +145,91 @@ def test_parse_samples(temp_directory, create_sample_tsv):
 
     with pytest.raises(ValueError):
         parse_samples(invalid_tsv_file)
+
+
+def test_convert_to_dictionary():
+    paired_reads = {("sample1", "sample1_R1.fastq", "sample1_R2.fastq"), ("sample2", "sample2_R1.fastq", "sample2_R2.fastq")}
+    unpaired_reads = {("sample3", "sample3_R1.fastq"), ("sample4", "sample4_R1.fastq")}
+
+    expected_dictionary = {
+        "sample1": {"R1": "sample1_R1.fastq", "R2": "sample1_R2.fastq"},
+        "sample2": {"R1": "sample2_R1.fastq", "R2": "sample2_R2.fastq"},
+        "sample3": {"R1": "sample3_R1.fastq", "R2": None},
+        "sample4": {"R1": "sample4_R1.fastq", "R2": None},
+    }
+
+    assert convert_to_dictionary(paired_reads, unpaired_reads) == expected_dictionary
+
+
+@pytest.mark.filterwarnings("ignore:Orphaned paired")
+def test_parse_samples_to_dictionary(temp_directory, create_sample_tsv):
+    # Test parsing a directory
+    directory_dictionary = {
+        "sample1": {"R1": os.path.join(temp_directory, "sample1_R1.fastq"), "R2": os.path.join(temp_directory, "sample1_R2.fastq")},
+        "sample2": {"R1": os.path.join(temp_directory, "sample2_R1_001.fastq.gz"), "R2": os.path.join(temp_directory, "sample2_R2_001.fastq.gz")},
+        "sample3": {"R1": os.path.join(temp_directory, "sample3.fastq"), "R2": None},
+        "sample4_R2": {"R1": os.path.join(temp_directory, "sample4_R2.fastq"), "R2": None},
+        "sample5": {"R1": os.path.join(temp_directory, "sample5.fasta.gz"), "R2": None},
+        "sample6": {"R1": os.path.join(temp_directory, "sample6.fastq.gz"), "R2": None},
+    }
+
+    assert parse_samples_to_dictionary(temp_directory) == directory_dictionary
+
+    # Test parsing a TSV file
+    tsv_dictionary = {
+        "sample1": {"R1": os.path.join(temp_directory, "sample1_R1.fastq"), "R2": os.path.join(temp_directory, "sample1_R2.fastq")},
+        "sample2": {"R1": os.path.join(temp_directory, "sample2_R1_001.fastq.gz"), "R2": os.path.join(temp_directory, "sample2_R2_001.fastq.gz")},
+        "sample3": {"R1": os.path.join(temp_directory, "sample3.fastq"), "R2": None},
+        "sample4_R2": {"R1": os.path.join(temp_directory, "sample4_R2.fastq"), "R2": None},
+        "sample5": {"R1": os.path.join(temp_directory, "sample5.fasta.gz"), "R2": None},
+        "sample6": {"R1": os.path.join(temp_directory, "sample6.fastq.gz"), "R2": None},
+    }
+
+    assert parse_samples_to_dictionary(create_sample_tsv) == tsv_dictionary
+
+    # Test parsing an invalid file or directory
+    invalid_path = os.path.join(temp_directory, "nonexistent_file.tsv")
+    with pytest.raises(ValueError):
+        parse_samples_to_dictionary(invalid_path)
+
+    invalid_path = os.path.join(temp_directory, "nonexistent_directory")
+    with pytest.raises(ValueError):
+        parse_samples_to_dictionary(invalid_path)
+
+    # Test parsing a TSV file with FileNotFoundError
+    invalid_tsv_file = os.path.join(temp_directory, "invalid_reads.tsv")
+    invalid_tsv_content = "sample1\tnonexistent_R1.fastq\t"
+
+    with open(invalid_tsv_file, "w") as tsv_file:
+        tsv_file.write(invalid_tsv_content)
+
+    with pytest.raises(ValueError):
+        parse_samples_to_dictionary(invalid_tsv_file)
+
+
+def test_write_samples_tsv(temp_directory):
+    samples_dictionary = {
+        "sample1": {"R1": os.path.join(temp_directory, "sample1_R1.fastq"), "R2": os.path.join(temp_directory, "sample1_R2.fastq")},
+        "sample2": {"R1": os.path.join(temp_directory, "sample2_R1_001.fastq.gz"), "R2": os.path.join(temp_directory, "sample2_R2_001.fastq.gz")},
+        "sample3": {"R1": os.path.join(temp_directory, "sample3.fastq"), "R2": None},
+        "sample4_R2": {"R1": os.path.join(temp_directory, "sample4_R2.fastq"), "R2": None},
+        "sample5": {"R1": os.path.join(temp_directory, "sample5.fasta.gz"), "R2": None},
+        "sample6": {"R1": os.path.join(temp_directory, "sample6.fastq.gz"), "R2": None},
+    }
+
+    output_file = os.path.join(temp_directory, "output.tsv")
+    write_samples_tsv(samples_dictionary, output_file)
+
+    with open(output_file, "r") as file:
+        content = file.read()
+
+    expected_content = (
+        "sample1\t" + os.path.join(temp_directory, "sample1_R1.fastq") + "\t" + os.path.join(temp_directory, "sample1_R2.fastq") + "\n"
+        "sample2\t" + os.path.join(temp_directory, "sample2_R1_001.fastq.gz") + "\t" + os.path.join(temp_directory, "sample2_R2_001.fastq.gz") + "\n"
+        "sample3\t" + os.path.join(temp_directory, "sample3.fastq") + "\tNone\n"
+        "sample4_R2\t" + os.path.join(temp_directory, "sample4_R2.fastq") + "\tNone\n"
+        "sample5\t" + os.path.join(temp_directory, "sample5.fasta.gz") + "\tNone\n"
+        "sample6\t" + os.path.join(temp_directory, "sample6.fastq.gz") + "\tNone\n"
+    )
+
+    assert content == expected_content