Metadata-Version: 2.1
Name: methrandir
Version: 0.0.3
Summary: Python utility for understanding whole genome bisulfite data and viewing it as a whole
Home-page: https://forgemia.inra.fr/skander.hatira/methrandir
Author: Skander Hatira
Author-email: skander.hatira@inrae.fr
License: UNKNOWN
Project-URL: Bug Tracker, https://forgemia.inra.fr/skander.hatira/methrandir/-/issues
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.8.5
Description-Content-Type: text/markdown
License-File: LICENSE

# Mehtrandir

## Installation

This package is available on [anaconda](https://anaconda.org/skanderPoit/methrandir) and can be installer with the following command

```bash
conda install -c skanderpoit methrandir
```

## Usage
Directly from the command line:
```bash
$ methrandir --help
usage: methrandir [-h] -f FILES [-o OUT_PREFIX] [-outdir OUTDIR] [-m METHOD]
                  [-c MIN_COVERAGE]

Methylation Data Overview Utility

optional arguments:
  -h, --help            show this help message and exit
  -f FILES, --files FILES
                        tab seperated file containing paths of sorted bismark
                        CX reports and their
  -o OUT_PREFIX, --out_prefix OUT_PREFIX
                        output files prefix
  -outdir OUTDIR, --outdir OUTDIR
                        output directory
  -m METHOD, --method METHOD
                        model biological replicates
  -c MIN_COVERAGE, --min_coverage MIN_COVERAGE
                        minimum number of reads for each position on all
                        samples
```
Or imported as a module in your python scri
```python
from methrandir import methrandir
```
methrandir.readlines() needs a `.tsv` file describing raw data(Sorted Bismark CX reports) and can take other arguments to further filter data for each position.

methrandir.compute_pca() takes in the product of readfiles and applies pca and generates some graphs.

