geneplexus 1.0.0.dev0

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GeneplexusPublic

A Python package of the GenePlexus analysis pipeline.

• The GenePlexus paper
• The repository for reproducing the experiments
• The webserver

Quick start

Installation

Install the GenePlexus package via pip.

pip install .

Run GenePlexus pipline

Example script

See example/example_run.py for example usage of the API.

Command-line interface

geneplexus --input_file example/input_genes.txt --output_dir result/ --data_dir data/

Full CLI options (check out with geneplexus --help)

Run the GenePlexus pipline on a input gene list.

optional arguments:
  -h, --help            show this help message and exit
  --input_file INPUT_FILE
                        Input gene list (.txt) file (one gene per line).
                        (default: None)
  --gene_list_delimiter GENE_LIST_DELIMITER
                        Delimiter used in the gene list. Use 'newline' if the
                        genes are separated by new line, and use 'tab' if the
                        genes are seperate by tabs. Other generic separator are
                        also supported, e.g. ', '. (default: newline)
  --network {BioGRID,STRING,STRING-EXP,GIANT-TN}
                        Network to use for generating features.
                        (default: BioGRID)
  --feature {Adjacency,Embedding,Influence}
                        Types of feature to use. (default: Embedding)
  --GSC {GO,DisGeNet}   Geneset collection used to generate negatives and the
                        model similarities. (default: GO)
  --small_edgelist_num_nodes SMALL_EDGELIST_NUM_NODES
                        Number of nodes in the small edgelist. (default: 50)
  --data_dir DATA_DIR   Directory in which the data are stored.
                        (default: data/)
  --output_dir OUTPUT_DIR
                        Output directory with respect to the repo root
                        directory. (default: result/)
  --zip_output          If set, then compress the output directory into a Tar
                        Gz file. (default: False)

Dev

Installation

Install the PyGenePlexus package in editable mode with dev dependencies

pip install -e ."[dev]"

Testing

Run the default test suite

pytest test/

By default, test data will be cached. Thus, after the first test run, data redownload will not be tested. To force redownload, specify the --cache-clear option

pytest test/ --cache-clear

Building Documentation

1. Install doc dependencies pip install -r docs/requirements.txt
2. Build

cd docs
make html

3. Open doc open build/html/index.html