From eed1cfa60fc5c8c9652919f977618d85660d85dd Mon Sep 17 00:00:00 2001 From: zhuchcn Date: Thu, 15 Jun 2023 15:01:15 -0700 Subject: [PATCH 1/3] doc (moPepGen): 1. version bump to 1.0.0; 2. added some badges 3. document the --chr issue in vignette --- CHANGELOG.md | 2 +- README.md | 5 ++++- docs/vignette.md | 4 ++++ moPepGen/__init__.py | 2 +- 4 files changed, 10 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 7478ddd5..6dc26db9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -10,7 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm ## [Unreleased] -## [0.12.0] - 2023-04-18 +## [1.0.0] - 2023-06-15 ### Added diff --git a/README.md b/README.md index 2fc46ca5..54e5d439 100644 --- a/README.md +++ b/README.md @@ -2,8 +2,11 @@ +[![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://img.shields.io/badge/Lifecycle-Maturing-007EC6) [![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml) -[![Docs](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/docs.yaml) +[![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen) +[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](uclahs-cds.github.io/private-moPepGen/) +[![License](https://img.shields.io/badge/License-GPLv2.0-blue)](#license "Go to license section") diff --git a/docs/vignette.md b/docs/vignette.md index 69791cf2..a9b352c7 100644 --- a/docs/vignette.md +++ b/docs/vignette.md @@ -59,6 +59,10 @@ Single nucleotide variants (SNVs/SNPs) and small insertions/deletions (INDELs) c Note that, the VEP cache files must be downloaded prior to running VEP (see [here](https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html)). The VEP developers recommend downloading the VEP cache version which corresponds to the Ensembl VEP installation. We also strongly recommend explicitly providing the exact reference genome and GTF file used in moPepGen to VEP to ensure the consistency of transcript IDs (i.e., using `--custom ${ANNOTATION_GTF},${REFERENCE_VERSION},gtf`). The exact genome FASTA and annotation GTF files should be used later when calling for variant peptides. +!!! warning + + If you use `--chr` to limit the chromosomes to annotate, make sure the style matches with your VCF/BED file. For example, if the chromosomes have the 'chr' prefix in your VCF file (*i.e.*, chr1, chr2, ...), you must include the prefix as well (*i.e.*, `--chr chr1,chr2,chr3`). + The example data does not work for VEP. ```shell diff --git a/moPepGen/__init__.py b/moPepGen/__init__.py index 73235ab9..87b412aa 100644 --- a/moPepGen/__init__.py +++ b/moPepGen/__init__.py @@ -5,7 +5,7 @@ from typing import Iterable, IO -__version__ = '0.12.0' +__version__ = '1.0.0' ## Error messages ERROR_INDEX_IN_INTRON = 'The genomic index seems to be in an intron' From 311c701ced1dfd483b0c8a8b325026bf1eca06e1 Mon Sep 17 00:00:00 2001 From: zhuchcn Date: Thu, 15 Jun 2023 15:07:21 -0700 Subject: [PATCH 2/3] doc (READEM): redirect licence badge to the license file --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 54e5d439..5e5139e3 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ [![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml) [![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen) [![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](uclahs-cds.github.io/private-moPepGen/) -[![License](https://img.shields.io/badge/License-GPLv2.0-blue)](#license "Go to license section") +[![License](https://img.shields.io/badge/License-GPL_v2-blue)](./LICENSE.txt) From 0caf57721ef99e5c9ca677e4607f8af85c375487 Mon Sep 17 00:00:00 2001 From: zhuchcn Date: Thu, 15 Jun 2023 15:08:37 -0700 Subject: [PATCH 3/3] doc (README): fix url for documenation badge --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5e5139e3..44c1c4cc 100644 --- a/README.md +++ b/README.md @@ -5,7 +5,7 @@ [![Lifecycle:Maturing](https://img.shields.io/badge/Lifecycle-Maturing-007EC6)](https://img.shields.io/badge/Lifecycle-Maturing-007EC6) [![Tests](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml/badge.svg)](https://github.com/uclahs-cds/private-moPepGen/actions/workflows/tests.yaml) [![Docker](https://img.shields.io/badge/docker-%230db7ed.svg?style=plastic&logo=docker&logoColor=white)](https://github.com/uclahs-cds/private-moPepGen/pkgs/container/mopepgen) -[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](uclahs-cds.github.io/private-moPepGen/) +[![Documentation](https://img.shields.io/static/v1?style=plastic&message=ReadTheDocs&color=2C4AA8&logo=ReadTheDocs&logoColor=FFFFFF&label=Documentation)](https://uclahs-cds.github.io/private-moPepGen/) [![License](https://img.shields.io/badge/License-GPL_v2-blue)](./LICENSE.txt)