pathme 0.1.6

Citation

If you use PathMe in your work, please consider citing:

Installation

1. pathme can be installed with the following commands:

$ python3 -m pip install git+https://github.com/ComPath/PathMe.git@master

2. or in editable mode with:

$ git clone https://github.com/ComPath/PathMe.git
$ cd pathme
$ python3 -m pip install -e .

How to Use

Before using PathMe, make sure you have installed and populated the Bio2BEL HGNC and Bio2BEL ChEBI databases (Simple run:”python3 -m bio2bel_hgnc populate” and “python3 -m bio2bel_chebi populate”) in your favourite terminal.

Each database has three main commands: download, bel, and summarize:

1. Download content

PathMe first requires to download the raw files from the original pathway databases. This can be accomplished by running the command (‘database’ can be either KEGG, Reactome, or WikiPathways). E.g., python3 -m pathme kegg download

$ python3 -m pathme <database> download

2. Generate BEL Graphs

Once the raw files are downloaded, you can run the following to command to generate BELGraphs that will be exported as Python pickles files for further analysis. Furthermore, the conversion to BEL can be tuned differently for each database by using specific commands. For example, KEGG parameters are shown when running “python3 -m pathme kegg bel –help”. Finally, please bear in mind that converting the Reactome files take up to 8 hours due to the large amount of its RDF file.

$ python3 -m pathme <database> bel

2. Summarize

Summarizes the result of the conversion to BEL.

$ python3 -m pathme <database> summarize

Advanced Parameters

KEGG Functionalities

The KEGG module of PathMe is able to handle KGML differently depending on the goal. By default, KEGG groups together the complex of nodes (e.g., gene families) into one node as it is depicted in the KEGG cartoons and represented in the KGML files. However, this behavior can be modified by adding the parameter –flatten=True in the exporting command. Example:

$ python3 -m pathme kegg bel --flatten

References