From 3f5f4a683cc765cbf8f2ba169a1dbd5f010d062a Mon Sep 17 00:00:00 2001 From: Malte Kuehl Date: Tue, 23 Jul 2024 21:58:00 +0200 Subject: [PATCH] Add Bioconda install badge --- README.md | 9 +++++---- docs/source/start.md | 9 +++++---- pytximport/core/_tximport.py | 2 +- 3 files changed, 11 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index f58f393..d2c9010 100755 --- a/README.md +++ b/README.md @@ -1,14 +1,15 @@ # pytximport [![Version](https://img.shields.io/pypi/v/pytximport)](https://pypi.org/project/pytximport/) -[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport) ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/complextissue/pytximport/ci.yml) [![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest) -[![codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport) +[![Codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport) +[![Install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pytximport/README.html) ![PyPI - Downloads](https://img.shields.io/pypi/dm/pytximport) -[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/) -[![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport) +[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) `pytximport` is a Python package for efficient gene count estimation based on transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `kallisto` or `salmon`. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html). diff --git a/docs/source/start.md b/docs/source/start.md index a93f429..a554f38 100755 --- a/docs/source/start.md +++ b/docs/source/start.md @@ -1,14 +1,15 @@ # Start [![Version](https://img.shields.io/pypi/v/pytximport)](https://pypi.org/project/pytximport/) -[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport) ![GitHub Actions Workflow Status](https://img.shields.io/github/actions/workflow/status/complextissue/pytximport/ci.yml) [![Documentation Status](https://readthedocs.org/projects/pytximport/badge/?version=latest)](https://pytximport.readthedocs.io/en/latest/?badge=latest) -[![codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport) +[![Codecov](https://codecov.io/gh/complextissue/pytximport/graph/badge.svg?token=M9JEHJVXYI)](https://codecov.io/gh/complextissue/pytximport) +[![Install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pytximport/README.html) ![PyPI - Downloads](https://img.shields.io/pypi/dm/pytximport) -[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) [![Python Version Required](https://img.shields.io/pypi/pyversions/pytximport)](https://pypi.org/project/pytximport/) -[![License](https://img.shields.io/pypi/l/pytximport)](https://github.com/complextissue/pytximport) +[![Code Style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) +[![pre-commit](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit) `pytximport` is a Python package for efficient gene count estimation based on transcript quantification files produced by pseudoalignment/quasi-mapping tools such as `kallisto` or `salmon`. `pytximport` is a port of the popular [tximport Bioconductor R package](https://bioconductor.org/packages/release/bioc/html/tximport.html). diff --git a/pytximport/core/_tximport.py b/pytximport/core/_tximport.py index e929158..fac374d 100644 --- a/pytximport/core/_tximport.py +++ b/pytximport/core/_tximport.py @@ -87,7 +87,7 @@ def tximport( abundance_column (Optional[str], optional): The column name for the abundance. Defaults to None. custom_importer (Optional[Callable], optional): A custom importer function. Defaults to None. existence_optional (bool, optional): Whether the existence of the files is optional. Defaults to False. - sparse (bool, optional): Whether to use sparse matrices. Currenlty, sparse input is not supported. + sparse (bool, optional): Whether to use sparse matrices. Currently, sparse input is not supported. Defaults to False. sparse_threshold (Optional[float], optional): The threshold for the sparse matrix. Currently, sparse input is not supported. Defaults to None.