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
validate-with-data
Run validation with RCR for a given network and experimental data.
drug2ways validate-with-data [OPTIONS]
Options
- -l, --log
Activate debug mode
- -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, --target <target>
Name of the drug to be used as target
- -t, --target <target>
Name of the drug to be used as source
- -f, --fmt <fmt>
Graph fmt
- Options
csv | tsv | graphml | bel | json | pickle
- -g, --graph <graph>
Required Path to the network