# methylink
[](https://github.com/projectoriented/methylink/actions?query=branch%3Amain+workflow%3ATests)
[](https://github.com/projectoriented/methylink/blob/main/LICENSE)
A command line tool to link methylated sites between two BAM/SAM files of the same origin.
## Installation
In a **clean** :sparkles: environment
```shell
pip install methylink
```
## Usage:
```shell
Usage: methylink [OPTIONS] COMMAND [ARGS]...
A command line tool to link methylated sites between two BAM files of the
same origin.
Options:
-h, --help Show this message and exit.
--version Show the version and exit.
--log_level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
Set the level of log output. [default:
INFO]
--threads INTEGER Number of threads to use. [default: 1]
--tmp PATH Temp directory to use.
--methyl_bams TEXT Unmapped bam files with methylation tags.
[required]
--aln TEXT Aligned bam to map the meth tags to.
[required]
--sample TEXT Sample name. [required]
--output TEXT Output file. [required]
```
## Quick start
```shell
methylink \
--threads 2 \
--aln tests/data/CHM1_aln_test-subsampled.bam \
--sample CHM1 \
--methyl_bams "$(echo tests/data/CHM1_methylated_test-{1,2,3,4,5}.bam)" \
--output CHM1-linked.bam
```
## Development
I'm happy with any contributions to make this code better :muscle:. You should be able to go forth with the following:
```shell
git clone [this repo]
cd methylink
python -m venv vmeth
source vmeth/bin/activate
pip install --editable .
```
## What remains to do-
- [ ] add to bioconda
- [ ] expand on documentation
- [x] use signal library to catch for forced exit (eg. ctrl+c) to safely delete temp folders
- [x] write github actions to automate test + build + publish
## Test
```shell
pytest
```
If that's okay then you're good to go, :tada:!
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"description": "\n# methylink\n[](https://github.com/projectoriented/methylink/actions?query=branch%3Amain+workflow%3ATests)\n[](https://github.com/projectoriented/methylink/blob/main/LICENSE)\n\nA command line tool to link methylated sites between two BAM/SAM files of the same origin.\n\n## Installation\nIn a **clean** :sparkles: environment\n```shell\npip install methylink\n```\n\n## Usage:\n```shell \nUsage: methylink [OPTIONS] COMMAND [ARGS]...\n\n A command line tool to link methylated sites between two BAM files of the\n same origin.\n\nOptions:\n -h, --help Show this message and exit.\n --version Show the version and exit.\n --log_level [DEBUG|INFO|WARNING|ERROR|CRITICAL]\n Set the level of log output. [default:\n INFO]\n --threads INTEGER Number of threads to use. [default: 1]\n --tmp PATH Temp directory to use.\n --methyl_bams TEXT Unmapped bam files with methylation tags.\n [required]\n --aln TEXT Aligned bam to map the meth tags to.\n [required]\n --sample TEXT Sample name. [required]\n --output TEXT Output file. [required]\n\n```\n\n## Quick start\n```shell\nmethylink \\\n --threads 2 \\\n --aln tests/data/CHM1_aln_test-subsampled.bam \\\n --sample CHM1 \\\n --methyl_bams \"$(echo tests/data/CHM1_methylated_test-{1,2,3,4,5}.bam)\" \\\n --output CHM1-linked.bam\n```\n\n## Development\nI'm happy with any contributions to make this code better :muscle:. You should be able to go forth with the following:\n```shell\ngit clone [this repo]\ncd methylink\npython -m venv vmeth\nsource vmeth/bin/activate\n\npip install --editable .\n```\n\n## What remains to do-\n- [ ] add to bioconda\n- [ ] expand on documentation\n- [x] use signal library to catch for forced exit (eg. ctrl+c) to safely delete temp folders\n- [x] write github actions to automate test + build + publish\n\n## Test\n```shell\npytest\n```\nIf that's okay then you're good to go, :tada:!\n",
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