diff --git a/README.md b/README.md index fb13f52c59bb0f7c9276cfd806734fc6fe21a315..bd0a6020412d823a30251c0fe912a6f25ac9f74e 100644 --- a/README.md +++ b/README.md @@ -197,152 +197,13 @@ The gui package exposes the command `cadbiom` to the current context. # Use -## Command line +## Command line & API -### General: +For up-to-date help on how to use the various commands, please visit this page: +[link](http://cadbiom.genouest.org/doc/cadbiom/command_line_usage.html) - $ cadbiom_cmd -h - - usage: cadbiom_cmd [-h] [-vv [VERBOSE]] - {compute_macs,sort_solutions,parse_trajectories,merge_cams} - ... - - optional arguments: - -h, --help show this help message and exit - -vv [VERBOSE], --verbose [VERBOSE] - - subcommands: - {compute_macs,sort_solutions,parse_trajectories,merge_cams} - compute_macs Parse arguments and launch Cadbiom search of MACs - (Minimal Activation Conditions). - If there is no - input file, there will be only one process. - If an - input file is given, there will be 1 process per line - (per logical formula on each line). - all_macs: Solver - will try to search all macs with 0 to the maximum of - steps allowed. - continue: If there is a mac file from - a previous work, last frontier places will be - reloaded. - sort_solutions Parse a solution file and sort all frontier places in - alphabetical order. - parse_trajectories Parse a complete solution file and make a - representation of trajectories. - The output is in graphml file format and is exported - in 'graphs' directory. .. note:: Requires the - model file. - merge_cams Merge solutions to a csv file. .. note:: CSV file: - <Final property formula>;<cam> - model_comp Model consistency checking. Check if the 2 given - models have the same topology, nodes & edges - attributes/roles. .. note:: You can export a graphml - file for the 2 models. - model_infos Model informations. Get number of nodes, edges, - centralities (degree, closeness, betweenness). .. - note:: You can export a graphml file for model. - - -### compute_macs: - - usage: cadbiom_cmd compute_macs [-h] [--input_file [INPUT_FILE]] - [--combinations] [--steps [STEPS]] - [--all_macs] [--continue] - [--start_prop [START_PROP]] - [--inv_prop [INV_PROP]] [--output [OUTPUT]] - chart_file [final_prop] - - positional arguments: - chart_file - final_prop - - optional arguments: - -h, --help show this help message and exit - --input_file [INPUT_FILE] - --combinations - --steps [STEPS] - --all_macs - --continue - --start_prop [START_PROP] - --inv_prop [INV_PROP] - --output [OUTPUT] - - -### parse_trajectories: - - usage: cadbiom_cmd parse_trajectories [-h] chart_file sol_file - - positional arguments: - chart_file - sol_file - -<br> -* Result: - -[image](examples/graph_example_with_legend.png) - -* Cytoscape styles: - -[file](examples/cytoscape_styles.xml) - - -### sort_solutions: - - usage: cadbiom_cmd sort_solutions [-h] sol_file - - positional arguments: - sol_file - - -### merge_cams: - - usage: cadbiom_cmd merge_cams [-h] [--output [OUTPUT]] [solutions_directory] - - positional arguments: - solutions_directory - - -### model_comp: - - usage: cadbiom_cmd model_comp [-h] [--make_graphs] model_file_1 model_file_2 - - positional arguments: - model_file_1 - model_file_2 - - optional arguments: - -h, --help show this help message and exit - --graphs - --json - --output [OUTPUT] - -<br> - -Usage in scripts: - - >>> from cadbiom_cmd.solution_repr import graph_isomorph_test - >>> print(graph_isomorph_test('test.bcx', 'test2.bcx', output_dir='graphs/', - make_graphs=False, make_json=False)) - INFO: 3 transitions loaded - INFO: 3 transitions loaded - INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0 - INFO: BUILD GRAPH FOR SOL: Connexin_32_0 Connexin_26_0 - INFO: Topology checking: True - INFO: Nodes checking: True - INFO: Edges checking: True - {u'nodes': True, u'edges': True, u'topology': True} - - -### model_infos - - usage: cadbiom_cmd model_infos [-h] [--graph] [--json] [--output [OUTPUT]] - model_file - - positional arguments: - model_file - - optional arguments: - -h, --help show this help message and exit - --graph - --json - --output [OUTPUT] +For up-to-date help on how to use the various APIs, please visit this page: +[link](http://cadbiom.genouest.org/doc/cadbiom/command_line_doc.html) ## Graphical User Interface