diff --git a/.gitignore b/.gitignore index 0a19790..0f6bd21 100644 --- a/.gitignore +++ b/.gitignore @@ -172,3 +172,6 @@ cython_debug/ # PyPI configuration file .pypirc + +*.DS_Store +src/.DS_Store diff --git a/pyproject.toml b/pyproject.toml index b7d9ace..6883b60 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [project] name = "HammingdistanceCalculator" -version = "0.1.0" +version = "0.2.0" description = "Script that calculates the hamming distance between a list of barcodes." readme = "README.md" authors = [ diff --git a/src/.DS_Store b/src/.DS_Store deleted file mode 100644 index fd73373..0000000 Binary files a/src/.DS_Store and /dev/null differ diff --git a/src/hammingdistancecalculator/hamming_distance.py b/src/hammingdistancecalculator/hamming_distance.py index 7132df2..9169dec 100644 --- a/src/hammingdistancecalculator/hamming_distance.py +++ b/src/hammingdistancecalculator/hamming_distance.py @@ -1,4 +1,3 @@ -import pathlib import re import typer import csv @@ -210,12 +209,18 @@ def compare_sample_barcode_list(sample_barcode_list: list) -> dict: # main script @cli.command() def main(input_csv: Path = typer.Argument(help="Pad naar input CSV met kolommen: label,barcode"), - max_distance: int = typer.Option( - 1, - "--max-distance", - "-d", - help="Maximale hamming distance waarvoor output wordt geschreven (default op 1, wat 0 & 1 schrijft)." - )): + max_distance: int = typer.Option( + 1, + "--max-distance", + "-d", + help="Maximale hamming distance waarvoor output wordt geschreven (default op 1, wat 0 & 1 schrijft)." + ), + outpath: Path = typer.Option( + ".", + "--outpath", + "-o", + help="Directory waar output files worden geschreven (default huidige directory)." + )): # read input sample_barcode_list = load_barcodes(input_csv) @@ -233,9 +238,15 @@ def main(input_csv: Path = typer.Argument(help="Pad naar input CSV met kolommen: for key, value in compare_dict.items(): hamming_distance_dict[value].append(key) - # write output files for all distances of 0 to max_distance (2 by default) - for counter in range(max_distance): - output_path = pathlib.Path(f"hamming_distance_{counter}.txt") + # verify output path exists to write to + outpath.mkdir(parents=True, exist_ok=True) + + # add 1 to the max distance because when you want a range of 1, you want to loop 'including' 1, not 'until' 1 + effective_max_distance = max_distance + 1 + + # write output files for all distances of 0 to effective_max_distance (2 by default) + for counter in range(effective_max_distance): + output_path = outpath / f"hamming_distance_{counter}.txt" # write each file with output_path.open('w', newline='') as file_handle: diff --git a/tests/test_hamming_distance.py b/tests/test_hamming_distance.py index 5b588ef..8bf79f6 100644 --- a/tests/test_hamming_distance.py +++ b/tests/test_hamming_distance.py @@ -1,6 +1,7 @@ import pytest import re from hammingdistancecalculator.hamming_distance import ( + cli, hamming_distance, is_valid_dna, rev_comp, @@ -8,6 +9,7 @@ load_barcodes, compare_sample_barcode_list ) +from typer.testing import CliRunner # test hamming distance function @pytest.mark.parametrize( @@ -153,7 +155,6 @@ def test_compare_sample_barcode_list_with_mocked_tpqm(mocker): progress_mock = mocker.MagicMock() tqdm_mock = mocker.MagicMock() tqdm_mock.return_value = progress_mock -# tqdm_mock.return_value.__enter__.return_value = progress_mock # patch the function we want to mock mocker.patch("hammingdistancecalculator.hamming_distance.tqdm", tqdm_mock) @@ -161,20 +162,6 @@ def test_compare_sample_barcode_list_with_mocked_tpqm(mocker): # store the return function so we can compare to the expected values return_value = compare_sample_barcode_list(test_set) - # - # # compare expected keys to return value - # expected_keys = { - # "S1_vs_S2", - # "S1_vs_revcomp_S2", - # "S1_vs_S3", - # "S1_vs_revcomp_S3", - # "S2_vs_S3", - # "S2_vs_revcomp_S3" - # } - # - # # check the keys are correct - # assert set(return_value.keys()) == expected_keys - # compare expected values to return values expected_values = { "S1_vs_S2": 1, @@ -193,4 +180,142 @@ def test_compare_sample_barcode_list_with_mocked_tpqm(mocker): # create tqdm & update it while going over the items # N = 3 -> total = N * (N - 1) = 6 - tqdm_mock.assert_called_once_with(total=6, desc="Compare_barcodes", unit="cmp") \ No newline at end of file + tqdm_mock.assert_called_once_with(total=6, desc="Compare_barcodes", unit="cmp") + + +def test_cli_outpath_parameter_creates_directory(tmp_path): + """Test dat --outpath directory automatisch maakt""" + input_file = tmp_path / "input.csv" + input_file.write_text("label,barcode\nS1,ACTG\nS2,ACCG", encoding="utf-8") + + output_dir = tmp_path / "custom_output" + assert not output_dir.exists() + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "--outpath", str(output_dir)]) + + assert result.exit_code == 0 + assert output_dir.exists(), "Directory werd niet aangemaakt!" + + +def test_cli_max_distance_plus_one_logic(tmp_path): + """Test dat max_distance+1 correct werkt (effectieve range telt 1 op bij max)""" + input_file = tmp_path / "data.csv" + input_file.write_text("label,barcode\nS1,AAAA\nS2,CCCC", encoding="utf-8") + + output_dir = tmp_path / "max_test" + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "-d", "2", "-o", str(output_dir)]) + + assert result.exit_code == 0 + + # max_distance=2, effectiveMaxDistance=3 → files 0, 1, 2 (3 files totaal) + created_files = sorted([f.name for f in output_dir.glob("hamming_distance_*.txt")]) + expected_files = ["hamming_distance_0.txt", "hamming_distance_1.txt", "hamming_distance_2.txt"] + + assert created_files == expected_files, f"Verwacht {expected_files}, kreeg {created_files}" + + +def test_cli_both_short_and_long_flags_work(tmp_path): + """Test dat zowel -d/-o als --max-distance/--outpath werken""" + input_file = tmp_path / "test.csv" + input_file.write_text("label,barcode\nX,ATGC\nY,ATGA", encoding="utf-8") + + output_dir = tmp_path / "flags_test" + + runner = CliRunner() + # Gebruik korte flags + result = runner.invoke(cli, [str(input_file), "-d", "1", "-o", str(output_dir)]) + + assert result.exit_code == 0 + assert len(list(output_dir.glob("*.txt"))) > 0 + + +def test_cli_default_behavior_without_options(tmp_path): + """Test default gedrag met expliciete . directory""" + input_file = tmp_path / "default.csv" + input_file.write_text("label,barcode\nA,ACTG\nB,ACCG", encoding="utf-8") + + output_dir = tmp_path / "dot_output" + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "-o", str(output_dir)]) + + assert result.exit_code == 0 + assert (output_dir / "hamming_distance_0.txt").exists() + + +def test_cli_help_shows_all_options(): + """Test dat --help beide opties toont""" + runner = CliRunner() + result = runner.invoke(cli, ["--help"]) + + assert result.exit_code == 0 + assert "--outpath" in result.stdout or "-o" in result.stdout + assert "--max-distance" in result.stdout or "-d" in result.stdout + + +def test_cli_multiple_barcodes_different_distances(tmp_path): + """Test met diverse afstanden tussen barcodes""" + input_file = tmp_path / "multi.csv" + # AAAA vs AAAA = dist 0 + # AAAA vs AAAA = dist 0 + # AAAA vs AAAG = dist 1 + # AAAA vs GGTC = dist 4 + input_file.write_text("label,barcode\nM,AAAA\nN,AAAA\nO,AAAG\nP,GGTC", encoding="utf-8") + + output_dir = tmp_path / "mixed_distances" + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "-d", "5", "-o", str(output_dir)]) + + assert result.exit_code == 0 + + # Minstens dist 0 en 1 moeten bestaan + assert (output_dir / "hamming_distance_0.txt").exists() + assert (output_dir / "hamming_distance_1.txt").exists() + + +def test_cli_output_content_verification(tmp_path): + """Test dat output file inhoud correct is""" + input_file = tmp_path / "verify.csv" + input_file.write_text("label,barcode\nFirst,AAAA\nSecond,AAAA", encoding="utf-8") + + output_dir = tmp_path / "content_check" + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "--outpath", str(output_dir)]) + + assert result.exit_code == 0 + + dist0 = output_dir / "hamming_distance_0.txt" + content = dist0.read_text() + + # Check juiste format (LET OP: "vs" met spaties, NIET "_vs_"!) + assert "Number of comparisons found with hamming distance 0:" in content + assert "Barcode First vs barcode Second" in content + assert "has hamming distance 0" in content + + +def test_cli_nonexistent_parent_directory_created(tmp_path): + """Test nested directory (parents=True)""" + input_file = tmp_path / "input.csv" + input_file.write_text("label,barcode\nS1,ACTG", encoding="utf-8") + + output_dir = tmp_path / "level1" / "level2" / "deep_output" + + runner = CliRunner() + result = runner.invoke(cli, [str(input_file), "-o", str(output_dir)]) + + assert result.exit_code == 0 + 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