From e32c10079b899da4e7ab3e3e6aac86f561c71c40 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Thu, 24 Oct 2024 09:37:27 +0200 Subject: [PATCH] Update readme (#140) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Fix #112 - change documentation link on README * changed a few more refs from Måns original url to new org url * action link --- CHANGELOG.md | 1 + CITATION.cff | 2 +- README.md | 90 ++++++++++++---------------------------------- docs/index.md | 14 ++++---- examples/readme.md | 18 +++++----- mkdocs.yml | 2 +- setup.py | 2 +- 7 files changed, 43 insertions(+), 86 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index f455062..8570432 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ Try to use the following format: - Fixed wrong models when chromosome X was named `chrX` and not `X` - Added GitHub Actions workflows for automatic publishing to PyPI on release, and keep a changelog reminder ([#136](https://github.com/Clinical-Genomics/genmod/pull/136)) - Optional user defined threshold and penalty for compound scoring +- Update README with current github.io docs page ## [3.8.3] diff --git a/CITATION.cff b/CITATION.cff index 25cf11f..35f31af 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -13,4 +13,4 @@ identifiers: type: doi value: "10.5281/zenodo.3841142" license: MIT Licence -repository-code: "https://github.com/moonso/genmod" +repository-code: "https://github.com/Clinical-Genomics/genmod" diff --git a/README.md b/README.md index 7d2be47..988758d 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3841142.svg)](https://doi.org/10.5281/zenodo.3841142) -[![Build Status](https://travis-ci.org/moonso/vcf_parser.svg)](https://travis-ci.org/moonso/genmod) +![Build Status - GitHub][actions-build-status] **GENMOD** is a simple to use command line tool for annotating and analyzing genomic variations in the [VCF](http://samtools.github.io/hts-specs/VCFv4.1.pdf) file format. @@ -17,7 +17,7 @@ The tools in the genmod suite are: - **genmod score**, Score the variants of a vcf based on their annotation - **genmod filter**, Filter the variants of a vcf based on their annotation -##Installation:## +## Installation **GENMOD** @@ -25,18 +25,16 @@ The tools in the genmod suite are: or - git clone https://github.com/moonso/genmod.git + git clone https://github.com/Clinical-Genomics/genmod.git cd genmod python setup.py install -## USAGE: ## +## Usage - -*This is an overview, for more in depth documentation see [documentation](http://moonso.github.io/genmod/)* +*This is an overview, for more in depth documentation see [documentation](https://Clinical-Genomics.github.io/genmod)* - -### Example: ### +### Example The following command should work when installed successfully. The files are distributed with the package. @@ -139,17 +137,18 @@ $genmod models -f/--family_file ``` - + + + +[actions-build-status]: https://github.com/Clinical-Genomics/genmod/actions/workflows/build_and_publish.yml/badge.svg diff --git a/docs/index.md b/docs/index.md index a21355e..d836a71 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,8 +1,8 @@ # Genmod #

- - + +

@@ -24,15 +24,15 @@ whole exome data and whole genome data. ## Installation ## **GENMOD** - +```bash pip install genmod - +``` or - - git clone https://github.com/moonso/genmod.git +```bash + git clone https://github.com/Clinical-Genomics/genmod.git cd genmod python setup.py install - +``` ### Example: ### diff --git a/examples/readme.md b/examples/readme.md index f911ca2..373fb71 100644 --- a/examples/readme.md +++ b/examples/readme.md @@ -12,9 +12,9 @@ If the user want to build own annotations please use **genmod build_annotation** ##Annotate variants for Recessive Family## - +``` genmod annotate examples/test_vcf.vcf -f examples/recessive_trio.ped -o examples/test_vcf_recessive_annotated.vcf - +``` The vcf file have a couple of variants made up so it will be easy to understand how the genetic inheritance patterns are annotated. With the basic command listed above the output should look like the variants in ```examples/test_vcf_recessive_annotated.vcf``` @@ -30,24 +30,24 @@ The following variants are to show how the ``-strict`` flag affects the analysis ##Annotate variants for Dominant Family## - +``` genmod annotate test_data/test_vcf.vcf -f test_data/dominant_trio.ped -o examples/test_vcf_dominant_annotated.vcf - +``` We can now see how the conditions change when one of the parents are affected. For example the recessive pattern for the first variant is not followed since all affected needs to be homozygote alternative if the variant should follow the Autosomal Recessive pattern. ##Annotate variants for Multiple Families## - +``` genmod annotate test_data/test_vcf.vcf -f test_data/multi_family.ped -o examples/test_vcf_multi_annotated.vcf - +``` We can now see how the conditions change when one of the parents are affected. For example the recessive pattern for the first variant is not followed since all affected needs to be homozygote alternative if the variant should follow the Autosomal Recessive pattern. ##Annotate variants with CADD scores and population frequencies## This is another example of how one can annotate with genmod: - +``` genmod annotate examples/test_vcf.vcf --cadd_file examples/small_CADD.tsv.gz --thousand_g examples/small_1000G.vcf.gz +``` - -Please post issues on http://github.com/moonso/genmod if any problems. \ No newline at end of file +Please post issues on http://github.com/Clinical-Genomics/genmod in case of any problems. \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 66f7579..65b095b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -3,7 +3,7 @@ site_name: genmod docs site_description: Project documentation with Markdown site_author: Måns Magnusson -repo_url: https://github.com/moonso/genmod +repo_url: https://github.com/Clinical-Genomics/genmod pages: - Home: index.md diff --git a/setup.py b/setup.py index 505644e..a61e5c0 100644 --- a/setup.py +++ b/setup.py @@ -24,7 +24,7 @@ description='Annotate genetic inheritance models in variant files', author = 'Mans Magnusson', author_email = 'mans.magnusson@scilifelab.se', - url = 'http://github.com/moonso/genmod', + url = 'http://github.com/Clinical-Genomics/genmod', license = 'MIT License', python_requires="~=3.8.0", install_requires=[