semvec/pypi-packages huggingface dataset:
methylink 0.6.0
methylink is a tool to link methylation tags between SAM/BAM files.
License: MIT
Requires Python: >=3.9.13
Keywords: methylation nanopore bioinformatics


# methylink
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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
```
**NOTE**: This does not work on windows. Separately, C libraries like zlib may be a dependency if you do not already have htslib installed- peep here: https://pysam.readthedocs.io/en/latest/installation.html#requirements. If a faster solution is desired and docker is installed, please build the image to circumvent local dependencies. Thanks!   

## 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. This will be a prefix for the output; e.g. CHM1-linked.bam [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:!