methrandir 0.0.1

Python utility for understanding whole genome bisulfite data and viewing it as a whole

Mehtrandir

Installation

This package is available on anaconda and can be installer with the following command

conda install -c skanderpoit methrandir

Usage

Directly from the command line:

$ 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

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.