diff --git a/.mypy.ini b/.mypy.ini index 7248bb12..c8f6d734 100644 --- a/.mypy.ini +++ b/.mypy.ini @@ -1,7 +1,7 @@ # Global options: [mypy] -python_version = 3.9 +python_version = 3.8 pretty = True warn_return_any = True warn_no_return = True diff --git a/coretex/bioinformatics/__init__.py b/coretex/bioinformatics/__init__.py index 36d2c9ee..8d551661 100644 --- a/coretex/bioinformatics/__init__.py +++ b/coretex/bioinformatics/__init__.py @@ -15,10 +15,10 @@ # You should have received a copy of the GNU Affero General Public License # along with this program. If not, see . -from typing import Optional, Union +from typing import Optional, Union, List from pathlib import Path -from .utils import CommandException, command +from .utils import command from ..coretex import CustomDataset @@ -64,7 +64,7 @@ def cutadaptTrim( if isinstance(reverseOutput, Path): reverseOutput = str(reverseOutput) - args: list[str] = [ + args: List[str] = [ "cutadapt", "-o", forwardOutput, "-g", forwardAdapter, diff --git a/coretex/bioinformatics/sequence_alignment/__init__.py b/coretex/bioinformatics/sequence_alignment/__init__.py index d1072f70..4d985eb0 100644 --- a/coretex/bioinformatics/sequence_alignment/__init__.py +++ b/coretex/bioinformatics/sequence_alignment/__init__.py @@ -187,9 +187,9 @@ def extractData(samtoolsPath: Path, file: Path) -> Tuple[List[int], List[int], L Link to samtools: http://htslib.org/ """ - scores: list[int] = [] - positions: list[int] = [] - sequenceLengths: list[int] = [] + scores: List[int] = [] + positions: List[int] = [] + sequenceLengths: List[int] = [] args = [ str(samtoolsPath.absolute()), @@ -238,7 +238,7 @@ def chmodX(file: Path) -> None: def loadFa(dataset: CustomDataset) -> List[Path]: - inputFiles: list[Path] = [] + inputFiles: List[Path] = [] for sample in dataset.samples: sample.unzip() diff --git a/coretex/coretex/sample/sequence_sample/local_sequence_sample.py b/coretex/coretex/sample/sequence_sample/local_sequence_sample.py index edb598a9..39a7557f 100644 --- a/coretex/coretex/sample/sequence_sample/local_sequence_sample.py +++ b/coretex/coretex/sample/sequence_sample/local_sequence_sample.py @@ -129,7 +129,7 @@ def isPairedEnd(self) -> bool: sampleContent = archive.namelist() for extension in self.supportedExtensions(): - fileNames: list[str] = [] + fileNames: List[str] = [] for fileName in sampleContent: if fileName.endswith(extension) or fileName.endswith(f"{extension}.gz"):