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https://github.com/cdcgov/snpeffr
R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net
https://github.com/cdcgov/snpeffr
clitool myco rpackage snpeff
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R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net
- Host: GitHub
- URL: https://github.com/cdcgov/snpeffr
- Owner: CDCgov
- License: apache-2.0
- Created: 2022-12-15T18:22:31.000Z (about 2 years ago)
- Default Branch: dev
- Last Pushed: 2024-08-23T15:27:24.000Z (4 months ago)
- Last Synced: 2024-08-23T17:25:01.296Z (4 months ago)
- Topics: clitool, myco, rpackage, snpeff
- Language: R
- Homepage:
- Size: 80.6 MB
- Stars: 0
- Watchers: 5
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: code-of-conduct.md
Awesome Lists containing this project
README
# snpeffr
The goal of the snpeffr package is to filter and parse outputs generated by snpeffr for MDB/Fungi Net.
It depends on the R packages `data.table` and `R.utils`. If using the command line
script included, you will also need the package `docopt`.
**Note that development happens on the dev branch to manage versions. The master branch is the legacy version of snpeffr maintained for backwards compatibility with
older versions of [mycosnp-nf](https://github.com/CDCgov/mycosnp-nf).**
## Installation
You can install the development version of snpeffr like so:
``` r
# if remotes not installed, then install the pkg
if(!require(remotes)) install.packages("remotes")
remotes::install_github("CDCgov/snpeffr@dev")
```
Or if you don't have git set up:
``` r
# install from zip location so no need for git
remotes::install_url("https://github.com/CDCgov/snpeffr/archive/refs/heads/dev.zip")
```
## Example
You can test out the function on the example data provided:
```{r example}
library(snpeffr)
# path to example vcf included in package
# replace with path to your vcf output if running on your own example
vcf_exe <- file.path(path.package("snpeffr"), "vcf-filter_ann_mod.vcf.gz")
# basic example
out <- snpeffr(vcf_path = vcf_exe)
head(out)
# to see function documentation/help for more details on the arguments and output
?snpeffr
```
## Command-line script
You can also use a command line version of this script at [inst/snpeffr.R](inst/snpeffr.R).
Download the file and from the directory where it's downloaded, run:
```
./snpeffr.R -f path_to_vcf
```
To get help and options for the command line version:
```
./snpeffr.R -h
```
Which will display the following help message:
```
Parse snpeff output to summary of mutations at positions of interest
Usage:
snpeffr.r [--fpath=FPATH] [--pos=POS] [--genes=GENES] [-exc=EXCL] [-out=OUT]
Options:
-v, --version Show version.
-f FPATH --fpath=FPATH path to input vcf file from snpeff
-p POS --pos=POS format as named comma separated list
of positions (no spaces), i.e. see default
[default: fks1_hs1=221638:221665,fks1_hs2=223782:223805]
-g GENES --genes=GENES a list of comma separated gene names (no spaces) [default: CAB11_002014]
-e EXCL --exc=EXCL a quoted regular expression for effects to exclude [default: 'synonymous_variant']
-o OUT --out=OUT csv or gz file to save output to [default: out.csv]
-h, --help show this help text
```
To set it up to run from anywhere in your environment, add the path to your .bashrc file:
```
export PATH=$PATH:path/to/snpeffr.R
```
## Docker image
There is a docker image to run snpeffr [here](https://github.com/CDCgov/snpeffr/pkgs/container/snpeffr), built off of rocker/r-ver.
It moves the command line script to the top level. To run inside docker use:
```
# and other associated commands
./snpeffr.R -h
```
## Next steps
- Use [snpsift](https://github.com/nf-core/modules/tree/master/modules/nf-core/snpsift) to do some of the upstream filtering (should be faster than reading in the
larger vcf using data.table, currently only the split command is a module, so we would
need to set up the filter command as a module if we wanted to use this.)
# CDCgov GitHub Organization Open Source Project
**General disclaimer** This repository was created for use by CDC programs to collaborate on public health related projects in support of the [CDC mission](https://www.cdc.gov/about/organization/mission.htm). GitHub is not hosted by the CDC, but is a third party website used by CDC and its partners to share information and collaborate on software. CDC use of GitHub does not imply an endorsement of any one particular service, product, or enterprise.
## Related documents
* [Open Practices](open_practices.md)
* [Rules of Behavior](rules_of_behavior.md)
* [Thanks and Acknowledgements](thanks.md)
* [Disclaimer](DISCLAIMER.md)
* [Contribution Notice](CONTRIBUTING.md)
* [Code of Conduct](code-of-conduct.md)
## Public Domain Standard Notice
This repository constitutes a work of the United States Government and is not
subject to domestic copyright protection under 17 USC § 105. This repository is in
the public domain within the United States, and copyright and related rights in
the work worldwide are waived through the [CC0 1.0 Universal public domain dedication](https://creativecommons.org/publicdomain/zero/1.0/).
All contributions to this repository will be released under the CC0 dedication. By
submitting a pull request you are agreeing to comply with this waiver of
copyright interest.
## License Standard Notice
The repository utilizes code licensed under the terms of the Apache Software
License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under
the terms of the Apache Software License version 2, or (at your option) any
later version.
This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the Apache Software License for more details.
You should have received a copy of the Apache Software License along with this
program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html
The source code forked from other open source projects will inherit its license.
## Privacy Standard Notice
This repository contains only non-sensitive, publicly available data and
information. All material and community participation is covered by the
[Disclaimer](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md)
and [Code of Conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).
For more information about CDC's privacy policy, please visit [http://www.cdc.gov/other/privacy.html](https://www.cdc.gov/other/privacy.html).
## Contributing Standard Notice
Anyone is encouraged to contribute to the repository by [forking](https://help.github.com/articles/fork-a-repo)
and submitting a pull request. (If you are new to GitHub, you might start with a
[basic tutorial](https://help.github.com/articles/set-up-git).) By contributing
to this project, you grant a world-wide, royalty-free, perpetual, irrevocable,
non-exclusive, transferable license to all users under the terms of the
[Apache Software License v2](http://www.apache.org/licenses/LICENSE-2.0.html) or
later.
All comments, messages, pull requests, and other submissions received through
CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at [http://www.cdc.gov/other/privacy.html](http://www.cdc.gov/other/privacy.html).
## Records Management Standard Notice
This repository is not a source of government records, but is a copy to increase
collaboration and collaborative potential. All government records will be
published through the [CDC web site](http://www.cdc.gov).
## Additional Standard Notices
Please refer to [CDC's Template Repository](https://github.com/CDCgov/template)
for more information about [contributing to this repository](https://github.com/CDCgov/template/blob/master/CONTRIBUTING.md),
[public domain notices and disclaimers](https://github.com/CDCgov/template/blob/master/DISCLAIMER.md),
and [code of conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md).