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https://github.com/chrovis/gnife
Gnife is a CLI tool for manipulating genomic files and data.
https://github.com/chrovis/gnife
bioinformatics clojure genomics
Last synced: about 1 month ago
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Gnife is a CLI tool for manipulating genomic files and data.
- Host: GitHub
- URL: https://github.com/chrovis/gnife
- Owner: chrovis
- License: apache-2.0
- Created: 2024-03-13T12:09:15.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2024-05-01T05:44:06.000Z (7 months ago)
- Last Synced: 2024-09-29T17:22:39.475Z (about 2 months ago)
- Topics: bioinformatics, clojure, genomics
- Language: Clojure
- Homepage:
- Size: 42 KB
- Stars: 1
- Watchers: 13
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
Awesome Lists containing this project
README
# Gnife [naɪf]
[](https://github.com/chrovis/gnife/actions/workflows/build.yml)
Gnife is a CLI tool for manipulating genomic files and data.
## Installation
### Manual Install
Gnife requires you have installed Java. A binary are available on the
[releases](https://github.com/chrovis/gnife/releases) page.
```sh
curl -sSL https://github.com/chrovis/gnife/releases/download/0.1.3/gnife -o gnife
chmod +x gnife
mv gnife [/your/PATH/dir/]
```
### Homebrew
You can use [Homebrew](https://brew.sh/) on MacOS.
```sh
brew install xcoo/formulae/gnife
```
### Build
To build Gnife manually, you must setup Clojure (and Java) in advance.
```sh
clojure -T:build bin
cp target/gnife [/your/PATH/dir/]
```
## Getting Started
Each Gnife command can be called by `gnife [type] [command]`.
```console
$ gnife hgvs repair "c.123_124GC>AA"
c.123_124delGCinsAA
```
## Command List
Gnife commands are grouped by data type. `gnife --tree` lists all commands in a
tree-like format.
```console
$ gnife --tree
sequence
dict Create a sequence dictionary for a reference sequence
faidx Index a reference sequence in the FASTA format
sam
view Extract/print all or sub alignments in SAM or BAM format
convert Convert file format based on the file extension
normalize Normalize references of alignments
sort Sort alignments by leftmost coordinates
index Index sorted alignment for fast random access
pileup Generate pileup for the BAM file
level Analyze a BAM file and add level information of alignments
vcf
liftover Convert genomic coordinates in a VCF file between assemblies
variant
liftover Convert a genomic coordinate between assemblies
to-hgvs Convert a VCF-style variant into HGVS
hgvs
format Format HGVS with a specified style
repair Repair an invalid HGVS
to-variant Convert a HGVS into VCF-style variants
```
`gnife [type] [command] --help` to display detailed usage of each command.
## JVM Options
To pass extra arguments to the JVM, set the `GNIFE_JVM_OPTS` environment
variable.
```sh
export GNIFE_JVM_OPTS="-XX:TieredStopAtLevel=1 -Xmx4g"
```
## Test
To run tests,
- `clojure -X:test` for basic tests, and
- `clojure -X:test:slow-test` for slow tests with remote resources.
## License
Copyright 2024 [Xcoo, Inc.](https://xcoo.jp/)
Licensed under the [Apache License, Version 2.0](LICENSE).