Command Line Interface¶

Drug2Ways Command Line Interface

drug2ways¶

drug2ways

drug2ways [OPTIONS] COMMAND [ARGS]...

combine¶

Run drug2ways for a given network and get sources that optimize given targets.

drug2ways combine [OPTIONS]

Options

-l, --log¶: Activate debug mode

-o, --output <output>¶: Output directory

-c, --combination-length <combination_length>¶: Required Combination length. Number of drugs in each combination.

-a, --activation-threshold <activation_threshold>¶: Activation threshold

--simple¶: Count only simple paths, i.e. paths without cycles.

-l, --lmax <lmax>¶: Required Maximum length of paths

-t, --targets <targets>¶: Path to file with source nodes

-s, --sources <sources>¶: Path to file with source nodes

-f, --fmt <fmt>¶

Graph fmt

Options: csv|tsv|graphml|bel|json|pickle

-g, --graph <graph>¶: Required Path to the network

explore¶

Run drug2ways for a given network.

drug2ways explore [OPTIONS]

Options

-t, --time¶: Export time measurements

-l, --log¶: Activate debug mode

-d, --drug-search-bel¶: Drug search for BEL graphs

-n, --name <name>¶: Name for output file

-o, --output <output>¶: Output directory

--simple¶: Count only simple paths, i.e. paths without cycles.

-l, --lmax <lmax>¶: Required Maximum length of paths

-t, --targets <targets>¶: Path to file with source nodes

-s, --sources <sources>¶: Path to file with source nodes

-f, --fmt <fmt>¶

Graph fmt

Options: csv|tsv|graphml|bel|json|pickle

-g, --graph <graph>¶: Required Path to the network

optimize¶

Run drug2ways for a given network and get sources that optimize given targets.

drug2ways optimize [OPTIONS]

Options

-l, --log¶: Activate debug mode

-o, --output <output>¶: Output directory

-a, --activation-threshold <activation_threshold>¶: Activation threshold

--simple¶: Count only simple paths, i.e. paths without cycles.

-l, --lmax <lmax>¶: Required Maximum length of paths

-t, --targets <targets>¶: Path to file with source nodes

-s, --sources <sources>¶: Path to file with source nodes

-f, --fmt <fmt>¶

Graph fmt

Options: csv|tsv|graphml|bel|json|pickle

-g, --graph <graph>¶: Required Path to the network

pathway-analysis¶

Run drug2ways pathway enrichment on the paths.

drug2ways pathway-analysis [OPTIONS]

Options

-l, --log¶: Activate debug mode

-o, --output <output>¶: Output directory

--simple¶: Count only simple paths, i.e. paths without cycles.

-l, --lmax <lmax>¶: Required Maximum length of paths

-t, --targets <targets>¶: Path to file with source nodes

-s, --sources <sources>¶: Path to file with source nodes

-f, --fmt <fmt>¶

Graph fmt

Options: csv|tsv|graphml|bel|json|pickle

-g, --graph <graph>¶: Required Path to the network