Introduction

Pattools is an advanced toolkit designed for the comprehensive analysis of Bisulfite sequencing (BS-Seq) data. This tool enables researchers to seamlessly evaluate a variety of DNA methylation metircs using BS-seq data and to implement algorithms developed by other researchers without the need for data format conversion.

• Pattools Document Website
• Github
• Open Issues

Development

1. Create a python 3.10+ environment, you can use conda, virtualenv, docker, etc. Or a local python environment (not recommended)
2. Install the project's dependent libraries

pip install -r requirements.txt

3. Deprecated Copy config.yaml.tpl to config.yaml and complete the configuration according to the local environment

Unit test

python -m unittest discover -s tests

or

python setup.py test

Installation

PyPI

pip install pattools-methy

Source code

Download the source code from the public repository Github

cd /path/to/source/code
python ./setup.py install

Install from private repository (Deprecated)

Install from the master branch

pip install git+https://e.coding.net/gomicsgene2/lung_cancer_yixing/pattools.git

Install from a feature branch

For example: install from dev-xxx branch

pip install git+https://e.coding.net/gomicsgene2/lung_cancer_yixing/pattools.git@dev-xxx

Usage (Deprecated, gradually moved to the docs directory)

pattools SDK

pattools toolkit

deconv

sun

pattools deconv -m sun -g hg38 \
    -c /mnt/d/project/wgbs_tools/references/hg38/CpG.bed.gz \
    -p /mnt/d/data/cacLung/raw/pat/GSM5652289_Blood-T-Eff-CD8-Z0000041F.hg38.pat.gz \
    --include  T-cells B-cells \
    -o /mnt/d/project/pattools/tmp/out.csv

moss

pattools deconv -m moss -g hg38 \
    -c /mnt/d/project/wgbs_tools/references/hg38/CpG.bed.gz \
    -p /mnt/d/data/cacLung/raw/pat/GSM5652289_Blood-T-Eff-CD8-Z0000041F.hg38.pat.gz \
    -o /mnt/d/project/pattools/tmp/out.csv

loyfer

pattools deconv -m loyfer -g hg38 -f Atlas.U25.l4.hg38.tsv\
    -c /mnt/d/project/wgbs_tools/references/hg38/CpG.bed.gz \
    -p /mnt/d/data/cacLung/raw/pat/GSM5652289_Blood-T-Eff-CD8-Z0000041F.hg38.pat.gz \
    -o /mnt/d/project/pattools/tmp/out.csv

entropy

pattools entropy -d 3 -w 4\
    -i /mnt/d/data/cacLung/raw/pat/GSM5652289_Blood-T-Eff-CD8-Z0000041F.hg38.pat.gz \
    -o /mnt/d/project/pattools/tmp/GSM5652289_Blood-T-Eff-CD8-Z0000041F.hg38.entropy

region

This command is used to convert a region between different coordinate systems, such as genome index coordinates or CpG index coordinates.

pattools region -t cpg2genome -i chr1:266762-266762 -c /mnt/d/project/wgbs_tools/references/hg38/CpG.bed.gz

region-file

pattools region-file -t cpg2genome --column col2  --out-format bed -c /mnt/d/project/wgbs_tools/references/hg38/CpG.bed.gz -i LUAD_1.0_0.txt -o LUAD_1.0_0.t.txt

License

Distributed under the MIT License. See LICENSE for more information.

Cite Us

Cheng et al. (2024). Novel diagnosis and therapeutic strategies for small cell lung cancer based on aberrant methylation in lung cancer subtypes. (journal not determined)

Acknowledgements

• wgbstools
• pysam
• samtools