Package: epiread-tools

Utils and conventions for using biscuit epiread files.

Usage

basic install

pip install git+https://github.com/methylgrammarlab/epiread-tools

alternatively, you may need to use an access token

pip install git+https://<PERSONAL ACCESS TOKEN>@github.com/methylgrammarlab/epiread-tools.git

you could also clone the repository and manually install

git clone https://<PERSONAL ACCESS TOKEN>@github.com/methylgrammarlab/epiread-tools.git
cd epiread-tools
python setup.py install

Configuration Parameters

The following parameters can be specified in the config dictionary or overwritten with specific arguments:

• cpg_coordinates (str): Path to the tab-delimited, gzipped file containing the coordinates of CpG sites.
• genomic_intervals (str): Intervals to process, either comma-delimited chrN:start-stop or a bed file.
• bedfile (bool): Set to True if the genomic intervals are in a bed file.
• header (bool): Set to True if the genomic intervals file has a header (only relevant if bedfile is True).
• epiread_files (list): List of gzipped epiread files.
• epiformat (str): Format of the epiread files. Currently, only supports old_epiread, old_epiread_A, and pat.
• outfile (str): Output file path for the generated bedgraph file.
• minimal_cpg_per_read (int): Minimum number of CpGs required per read. Default is 1.

All parameters can be specified with a config.json file, and specific arguments can overwrite the JSON file.

convert epiread to bedgraph

epireadToBedgraph -j <config.json>

If you combine json with command line agruments. e.g.:

epireadToBedgraph -j <config.json> --outfile=<output_file> -i chr3:50-150,ch10:440-450

The JSON will override the command line arguments.

To parse epiread with cpg coordinates use flag -A

if for some reason that doesn't work (Command not found), just find the script with

pip show epiread_tools

and run

python3 epireadToBedgraph.py -j <config.json>