diff --git a/meteor/counter.py b/meteor/counter.py index 6ebf8a8..57ba37f 100644 --- a/meteor/counter.py +++ b/meteor/counter.py @@ -85,7 +85,7 @@ def launch_mapping(self) -> None: ) mapping_process.execute() - def write_table(self, cramfile: Path, outfile: Path) -> None: + def write_table(self, cramfile: Path, outfile: Path) -> int: """Function that create a count table using pysam. First index the cram file, then count reads using the function idxstats from pysam, and output a count table. @@ -351,7 +351,7 @@ def compute_abs(self, unique_dict: dict, multiple_dict: dict) -> dict: genes: unique_dict[genes] + multiple_dict[genes] for genes in unique_dict } - def write_stat(self, output: Path, abundance_dict: dict, database: dict) -> None: + def write_stat(self, output: Path, abundance_dict: dict, database: dict) -> int: """Write count table. :param output: [STRING] = output filename diff --git a/meteor/session.py b/meteor/session.py index 5098dbb..8f4cd1d 100644 --- a/meteor/session.py +++ b/meteor/session.py @@ -34,7 +34,7 @@ class Component: DEFAULT_GAP_CHAR: ClassVar[str] = "N" DEFAULT_CORE_SIZE: ClassVar[int] = 100 - threads: int | None + threads: int fastq_dir: Path = field(default_factory=Path) mapping_dir: Path = field(default_factory=Path) profile_dir: Path = field(default_factory=Path) diff --git a/pyproject.toml b/pyproject.toml index 100e446..9fe1e40 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,7 +23,7 @@ packages = [ meteor = "meteor.meteor:main" [tool.poetry.dependencies] -python = ">=3.10,<3.13" +python = "^3.10" pandas = "^2.1.2" pysam = "^0.22.0" packaging = "^23.2"