methylink is a tool to link methylation tags between SAM/BAM files.
Project description
methylink
A command line tool to link methylated sites between two BAM/SAM files of the same origin.
Installation
In a clean :sparkles: environment
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:
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
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:
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
- use signal library to catch for forced exit (eg. ctrl+c) to safely delete temp folders
- write github actions to automate test + build + publish
Test
pytest
If that's okay then you're good to go, :tada:!
Project details
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