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