From 73a9cf41fce6886b361b7725e3f41e41825ba5a6 Mon Sep 17 00:00:00 2001 From: gpas-github-bot Date: Tue, 21 Jan 2025 13:42:21 +0000 Subject: [PATCH 01/10] fix: enhanced client side fastq validation --- pyproject.toml | 1 + src/pathogena/models.py | 46 ++++++++++++++++++++++---------- src/pathogena/util.py | 52 ------------------------------------ tests/test_util.py | 16 ------------ uv.lock | 58 +++++++++++++++++++++++++++++++++++++++++ 5 files changed, 91 insertions(+), 82 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 8954fcb..272c2c3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -29,6 +29,7 @@ dependencies = [ "pydantic>=2.6.2,<3", "tenacity==8.2.3", "click>=8.1.7", + "fastq-validation==1.0.2", ] [project.scripts] diff --git a/src/pathogena/models.py b/src/pathogena/models.py index c75c90a..f9130b4 100644 --- a/src/pathogena/models.py +++ b/src/pathogena/models.py @@ -3,6 +3,7 @@ from pathlib import Path from typing import Any, Literal, Optional +import fastq_validation from pydantic import BaseModel, Field, model_validator from pathogena import util @@ -168,19 +169,36 @@ def validate_reads_from_fastq(self) -> None: """ reads = self.get_read_paths() logging.info("Performing FastQ checks and gathering total reads") - valid_lines_per_read = 4 - self.reads_in = 0 - for read in reads: - logging.info(f"Calculating read count in: {read}") - if read.suffix == ".gz": - line_count = util.reads_lines_from_gzip(file_path=read) + try: + if self.is_illumina(): + stats1, stats2 = fastq_validation.check_illumina(*reads) + self.reads_in = stats1.num_reads + stats2.num_reads + if not stats1.is_illumina(): + raise ValueError( + f"FastQ file {reads[0]} doesn't appear to be Illumina! " + f"Mean read length {stats1.mean_read_length} bp, " + f"Percentage of reads the same length {round(stats1.percent_same_length * 100, 2)}%" + ) + if not stats2.is_illumina(): + raise ValueError( + f"FastQ file {reads[1]} doesn't appear to be Illumina! " + f"Mean read length {stats2.mean_read_length} bp, " + f"Percentage of reads the same length {round(stats2.percent_same_length * 100, 2)}%" + ) else: - line_count = util.reads_lines_from_fastq(file_path=read) - if line_count % valid_lines_per_read != 0: - raise ValueError( - f"FASTQ file {read.name} does not have a multiple of 4 lines" - ) - self.reads_in += line_count / valid_lines_per_read + stats = fastq_validation.check_ont(*reads) + self.reads_in = stats.num_reads + if not stats.is_ont(): + raise ValueError( + f"FastQ file {reads[0]} doesn't appear to be ONT! " + f"Mean read length {stats.mean_read_length} bp, " + f"Percentage of reads the same length {round(stats.percent_same_length * 100, 2)}%" + ) + except Exception as e: + logging.info(e) + raise ValueError( + f"Invalid FastQ file(s) for sample {self.sample_name}. Please check the file(s) and try again." + ) from e logging.info(f"{self.reads_in} reads in FASTQ file") def get_read_paths(self) -> list[Path]: @@ -189,9 +207,9 @@ def get_read_paths(self) -> list[Path]: Returns: list[Path]: A list of paths to the read files. """ - reads = [self.reads_1_resolved_path] + reads = [self.reads_1_resolved_path.as_posix()] if self.is_illumina(): - reads.append(self.reads_2_resolved_path) + reads.append(self.reads_2_resolved_path.as_posix()) return reads def is_ont(self) -> bool: diff --git a/src/pathogena/util.py b/src/pathogena/util.py index 17a5e4d..3587cad 100644 --- a/src/pathogena/util.py +++ b/src/pathogena/util.py @@ -431,58 +431,6 @@ def gzip_file(input_file: Path, output_file: str) -> Path: return Path(output_file) -def reads_lines_from_gzip(file_path: Path) -> int: - """Count the number of lines in a gzipped file. - - Args: - file_path (Path): The path to the gzipped file. - - Returns: - int: The number of lines in the file. - """ - line_count = 0 - # gunzip offers a ~4x faster speed when opening GZip files, use it if we can. - if command_exists("gunzip"): - logging.debug("Reading lines using gunzip") - result = subprocess.run( - ["gunzip", "-c", file_path.as_posix()], stdout=subprocess.PIPE, text=True - ) - line_count = result.stdout.count("\n") - if line_count == 0: # gunzip didn't work, try the long method - logging.debug("Using gunzip failed, using Python's gzip implementation") - try: - with gzip.open(file_path, "r") as contents: - line_count = sum(1 for _ in contents) - except gzip.BadGzipFile as e: - logging.error(f"Failed to open the Gzip file: {e}") - return line_count - - -def reads_lines_from_fastq(file_path: Path) -> int: - """Count the number of lines in a FASTQ file. - - Args: - file_path (Path): The path to the FASTQ file. - - Returns: - int: The number of lines in the file. - """ - try: - with open(file_path) as contents: - line_count = sum(1 for _ in contents) - return line_count - except PermissionError: - logging.error( - f"You do not have permission to access this file {file_path.name}." - ) - except OSError as e: - logging.error(f"An OS error occurred trying to open {file_path.name}: {e}") - except Exception as e: - logging.error( - f"An unexpected error occurred trying to open {file_path.name}: {e}" - ) - - def find_duplicate_entries(inputs: list[str]) -> list[str]: """Return a list of items that appear more than once in the input list. diff --git a/tests/test_util.py b/tests/test_util.py index 5ce4866..f630102 100644 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -3,22 +3,6 @@ from pathogena import util -def test_reads_lines_from_gzip() -> None: - """Test that the `reads_lines_from_gzip` function correctly reads the expected number of lines from a gzip file.""" - expected_lines = 4 - file_path = Path(__file__).parent / "data" / "reads" / "tuberculosis_1_1.fastq.gz" - lines = util.reads_lines_from_gzip(file_path=file_path) - assert lines == expected_lines - - -def test_reads_lines_from_fastq() -> None: - """Test that the `reads_lines_from_fastq` function correctly reads the expected number of lines from a fastq file.""" - expected_lines = 4 - file_path = Path(__file__).parent / "data" / "reads" / "tuberculosis_1_1.fastq" - lines = util.reads_lines_from_fastq(file_path=file_path) - assert lines == expected_lines - - def test_fail_command_exists() -> None: """Test that the `command_exists` function correctly identifies a non-existent command.""" assert not util.command_exists("notarealcommandtest") diff --git a/uv.lock b/uv.lock index f905860..b779003 100644 --- a/uv.lock +++ b/uv.lock @@ -152,6 +152,62 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/02/cc/b7e31358aac6ed1ef2bb790a9746ac2c69bcb3c8588b41616914eb106eaf/exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b", size = 16453 }, ] +[[package]] +name = "fastq-validation" +version = "1.0.2" +source = { registry = "https://pypi.org/simple" } +sdist = { url = "https://files.pythonhosted.org/packages/31/c6/4a588aefe3262c36fb7f31869d7708089fc046d56b262fff7454c7b0f61d/fastq_validation-1.0.2.tar.gz", hash = "sha256:8afc701845bd9fb44081a57f60d6a90b2fc7e4776302ef5a9971b1f249bed600", 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[PATCH 02/10] fix: clean up --- src/pathogena/util.py | 16 ---------------- tests/test_util.py | 5 ----- 2 files changed, 21 deletions(-) diff --git a/src/pathogena/util.py b/src/pathogena/util.py index 3587cad..d018fe7 100644 --- a/src/pathogena/util.py +++ b/src/pathogena/util.py @@ -394,22 +394,6 @@ def display_cli_version() -> None: logging.info(f"EIT Pathogena client version {pathogena.__version__}") -def command_exists(command: str) -> bool: - """Check if a command exists in the system. - - Args: - command (str): The command to check. - - Returns: - bool: True if the command exists, False otherwise. - """ - try: - result = subprocess.run(["type", command], capture_output=True) - except FileNotFoundError: # Catch Python parsing related errors - return False - return result.returncode == 0 - - def gzip_file(input_file: Path, output_file: str) -> Path: """Gzip a file and save it with a new name. diff --git a/tests/test_util.py b/tests/test_util.py index f630102..a028278 100644 --- a/tests/test_util.py +++ b/tests/test_util.py @@ -3,11 +3,6 @@ from pathogena import util -def test_fail_command_exists() -> None: - """Test that the `command_exists` function correctly identifies a non-existent command.""" - assert not util.command_exists("notarealcommandtest") - - def test_find_duplicate_entries() -> None: """Test that the `find_duplicate_entries` function correctly identifies duplicate entries in a list.""" data = ["foo", "foo", "bar", "bar", "baz"] From c6da0b98bfac597f2e5834c74ea700b7f4033e64 Mon Sep 17 00:00:00 2001 From: gpas-github-bot Date: Tue, 21 Jan 2025 13:55:18 +0000 Subject: [PATCH 03/10] style: fix type hint --- src/pathogena/models.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/pathogena/models.py b/src/pathogena/models.py index f9130b4..ba67379 100644 --- a/src/pathogena/models.py +++ b/src/pathogena/models.py @@ -201,11 +201,11 @@ def validate_reads_from_fastq(self) -> None: ) from e logging.info(f"{self.reads_in} reads in FASTQ file") - def get_read_paths(self) -> list[Path]: + def get_read_paths(self) -> list[str]: """Get the paths of the read files. Returns: - list[Path]: A list of paths to the read files. + list[str]: A list of paths to the read files. 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b/.github/workflows/test.yml index cbfad79..6ef0e36 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -28,9 +28,9 @@ jobs: shell: bash -el {0} run: | if [ "${{ matrix.os }}" == "ubuntu-22.04" ]; then - conda create -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} + conda create -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust==1.84.0 elif [ "${{ matrix.os }}" == "macos-14" ]; then - conda create --platform osx-64 -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} + conda create --platform osx-64 -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust==1.84.0 fi conda activate pathogena-test pip install '.[dev]' From d1d67a3c5b5d91df1ddb6f7b931ca76ef462b505 Mon Sep 17 00:00:00 2001 From: gpas-github-bot Date: Tue, 21 Jan 2025 20:30:23 +0000 Subject: [PATCH 09/10] fix: conda no rust version --- .github/workflows/test.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 6ef0e36..a365476 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -28,9 +28,9 @@ jobs: shell: bash -el {0} run: | if [ "${{ matrix.os }}" == "ubuntu-22.04" ]; then - conda create -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust==1.84.0 + conda create -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust elif [ "${{ matrix.os }}" == "macos-14" ]; then - conda create --platform osx-64 -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust==1.84.0 + conda create --platform osx-64 -y -n pathogena-test -c conda-forge -c bioconda hostile==1.1.0 python==${{ matrix.python-version }} rust fi conda activate pathogena-test pip install '.[dev]' From 1fb6562ee5edb2be93d268b42c4a02484a52dff0 Mon Sep 17 00:00:00 2001 From: gpas-github-bot Date: Wed, 22 Jan 2025 09:24:37 +0000 Subject: [PATCH 10/10] ci: try test with just macos --- .github/workflows/test.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a365476..dfb7a5c 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -13,7 +13,8 @@ jobs: runs-on: ${{ matrix.os }} strategy: matrix: - os: [ubuntu-22.04, macos-14] + # os: [ubuntu-22.04, macos-14] + os: [macos-14] python-version: ['3.10'] name: Python ${{ matrix.python-version }} (${{ matrix.os }}) steps: