Command line usage

Cadbiom - Command Line Interface

usage: cadbiom_cmd [-h] [-vv [VERBOSE]] [-V]
                   {solutions_search,solutions_sort,solutions_2_graphs,queries_2_json,json_2_interaction_graph,queries_2_common_graph,queries_2_occcurrence_matrix,queries_2_clustermap,merge_macs,model_identifier_mapping,model_comparison,model_info,model_graph}
                   ...

Named Arguments

-vv, --verbose	Default: “info”
-V, --version	show program’s version number and exit

subcommands

subcommand

Possible choices: solutions_search, solutions_sort, solutions_2_graphs, queries_2_json, json_2_interaction_graph, queries_2_common_graph, queries_2_occcurrence_matrix, queries_2_clustermap, merge_macs, model_identifier_mapping, model_comparison, model_info, model_graph

Sub-commands:

solutions_search

Launch the search for Minimum Activation Conditions (MAC) for entities

of interest.

cadbiom_cmd solutions_search [-h] [--output [OUTPUT]] [--steps [STEPS]] [--limit [LIMIT]]
                             [--continue] [--input_file [INPUT_FILE]] [--combinations]
                             [--start_prop [START_PROP]] [--inv_prop [INV_PROP]]
                             model_file [final_prop]

I/O

model_file	Cadbiom model (.bcx file).
--output	Output directory. Default: “result/”

Search settings

--steps	Maximum of allowed steps to find macs Default: 7
--limit	Limit the number of solutions. Default: 400
--continue	Resume previous computations; if there is a mac file from a previous work, last frontier places/boundaries will be reloaded. Default: False

Model checking

final_prop	Final property that will occur at the end of the simulation.
--input_file	Replace ‘final_prop’ argument by a file with 1 logical formula per line. This allows the software to launch 1 process per formula.
--combinations	If input_file is set, we can compute the combinations of the formulas indicated on each line. Default: False
--start_prop	Property that will be part of the initial state of the model. In concrete terms, some entities can be activated by this mechanism without modifying the model.
--inv_prop	Invariant property that will always occur during the simulation. The given logical formula will be checked at each step of the simulation.

Examples:

$ cadbiom_cmd solutions_search model_pid.bcx SRP9 –steps 10 –output ./SRP9_solutions/ $ cadbiom_cmd solutions_search model_pid.bcx –input_file my_queries.txt –output

solutions_sort

Read a solution file or a directory containing MAC solutions files

(mac files), and sort all frontier places/boundaries in alphabetical order.

cadbiom_cmd solutions_sort [-h] path

Positional Arguments

path	Solution file or directory with MAC solutions files (mac files) generated with the ‘solutions_search’ command.

solutions_2_graphs

Create GraphML formated files containing a representation of the

trajectories for each solution in complete MAC files (*mac_complete files).

This is a function to visualize paths taken by the solver from the boundaries to the entities of interest.

cadbiom_cmd solutions_2_graphs [-h] [--output [OUTPUT]] model_file path

I/O

model_file	Cadbiom model (.bcx file).
path	Complete solution file or directory with MAC solutions files (*mac_complete.txt files) generated with the ‘solutions_search’ command.
--output	Output directory for GraphML files. Default: “graphs/”

queries_2_json

Create a JSON formated file containing all data from complete MAC files

(*mac_complete files). The file will contain frontier places/boundaries and decompiled steps with their respective events for each solution.

This is a function to quickly search all transition attributes involved in a solution.

cadbiom_cmd queries_2_json [-h] [--output [OUTPUT]] [--no_conditions] model_file path

Named Arguments

--no_conditions
	Don’t export conditions of transitions. This allows to have only places/entities that are used inside trajectories; thus, inhibitors nodes are not present in the json file Default: False

I/O

model_file	Cadbiom model (.bcx file).
path	Complete solution file or directory with MAC solutions files (*mac_complete.txt files) generated with the ‘solutions_search’ command.
--output	Directory for newly created files. Default: “decompiled_solutions/”

json_2_interaction_graph

Make an interaction weighted graph based on the searched molecule of interest.

Read decompiled solutions files (.json files produced by the directive ‘queries_2_json’) and make a graph of the relationships between one or more molecules of interest, the genes and other frontier places/boundaries found among all the solutions.

cadbiom_cmd json_2_interaction_graph [-h] [--path [PATH]] [--output [OUTPUT]]
                                     molecules_of_interest [molecules_of_interest ...]

Positional Arguments

molecules_of_interest
	One or multiple molecule of interest to search in the trajectories of every solutions

Named Arguments

--path	JSON formated file containing all data from complete MAC files(*mac_complete files) generated with the ‘queries_2_json’ command. Default: “decompiled_solutions/”
--output	Directory for the newly created file. Default: “graphs/”

queries_2_common_graph

Create a GraphML formated file containing a unique representation of all

trajectories corresponding to all solutions in each complete MAC file (*mac_complete files).

This is a function to visualize paths taken by the solver from the boundaries to the entities of interest.

cadbiom_cmd queries_2_common_graph [-h] [--graphs] [--csv] [--json] [--output [OUTPUT]]
                                   model_file path

I/O

model_file	Cadbiom model (.bcx file).
path	Complete solution file or directory with MAC solutions files (*mac_complete.txt files) generated with the ‘solutions_search’ command.
--graphs	Create a GraphML file for each MAC file. Default: False
--csv	Create a CSV file containing a summary about places/entities of the solutions. Default: False
--json	Create a JSON formated file containing a summary about places/entities of the solutions. Default: False
--output	Output directory for GraphML files. Default: “graphs/”

queries_2_occcurrence_matrix

Create a matrix of occurrences counting entities in the solutions found in

*mac.txt files in the given path.

cadbiom_cmd queries_2_occcurrence_matrix [-h] [--output [OUTPUT]] [--transpose_csv]
                                         model_file path

Named Arguments

--transpose_csv
	Transpose the final matrix (switch columns and rows). Default: False

I/O

model_file	Cadbiom model (.bcx file).
path	Directory with MAC solutions files (*mac.txt files) generated with the ‘solutions_search’ command.
--output	Output directory for CSV files. Default: “./”

queries_2_clustermap

Create a ClusterMap (hierarchically-clustered heatmap) for boundaries

found in all the solutions stored in each *mac.txt file in the given path.

This is a function to visualize co-occurrences of the boundaries within the solutions obtained.

cadbiom_cmd queries_2_clustermap [-h] [--output [OUTPUT]] path

I/O

path	Directory with MAC solutions files or MAC file(*mac.txt files) generated with the ‘solutions_search’ command.
--output	Output directory for CSV and SVG files. Default: “./”

merge_macs

Merge solutions to a csv file.

cadbiom_cmd merge_macs [-h] [--output [OUTPUT]] [solutions_directory]

Positional Arguments

solutions_directory
	Default: “result/”

Named Arguments

--output

Directory for the CSV file merged_macs.csv; Structure: <Final property formula>;<mac> Default: “result/”

model_identifier_mapping

Mapping of identifiers from external databases.

This function exports a CSV formated file presenting the list of known Cadbiom identifiers for each given external identifier.

cadbiom_cmd model_identifier_mapping [-h]
                                     (--external_file EXTERNAL_FILE | --external_identifiers EXTERNAL_IDENTIFIERS [EXTERNAL_IDENTIFIERS ...])
                                     model_file

I/O

model_file	Cadbiom model (.bcx file).
--external_file
	File with 1 external identifiers to be mapped per line.
--external_identifiers
	Multiple external identifiers to be mapped.

model_comparison

Isomorphism test.

Check if the graphs based on the two given models have the same topology, nodes & edges attributes/roles.

cadbiom_cmd model_comparison [-h] [--graphs] [--json] [--output [OUTPUT]]
                             model_file_1 model_file_2

Positional Arguments

model_file_1	Cadbiom model (.bcx file).
model_file_2	Cadbiom model (.bcx file).

Named Arguments

--graphs	Create two GraphML files from the given models. Default: False
--json	Create a summary dumped into a json file. Default: False
--output	Directory for created graphs files. Default: “graphs/”

model_info

Provide several levels of information about the structure of the model

and its places/entities.

cadbiom_cmd model_info [-h]
                       (--default | --all_entities | --boundaries | --genes | --smallmolecules)
                       [--csv] [--json] [--output [OUTPUT]]
                       model_file

I/O

model_file	Cadbiom model (.bcx file).
--csv	Create a CSV file containing data about previously filtered places/entities of the model. Default: False
--json	Create a JSON formated file containing data about previously filtered places/entities of the model, and a full summary about the model itself (boundaries, transitions, events, entities locations, entities types). Default: False
--output	Directory for newly created files. Default: “./”

Filters

--default	Display quick description of the model (Number of places/entities, transitions, entity types, locations) Default: False
--all_entities	Retrieve data for all places/entities of the model. Default: False
--boundaries	Retrieve data only for the frontier places/boundaries of the model. Default: False
--genes	Retrieve data only for the genes in the model. Default: False
--smallmolecules
	Retrieve data only for the smallmolecules in the model. Default: False

model_graph

Information about the graph based on the model.

Get centralities (degree). Forge a GraphML file.

cadbiom_cmd model_graph [-h] [--centralities] [--graph] [--json] [--json_graph]
                        [--output [OUTPUT]]
                        model_file

Named Arguments

--centralities

Get centralities for each node of the graph (degree, in_degree, out_degree, closeness, betweenness). Works in conjunction with the --json option. Default: False

I/O

model_file	Cadbiom model (.bcx file).
--graph	Translate the model into a GraphML formated file which can be opened in Cytoscape. Default: False
--json	Create a JSON formated file containing a summary of the graph based on the model. Default: False
--json_graph	Create a JSON formated file containing the graph based on the model, which can be opened by Web applications. Default: False
--output	Directory for newly created files. Default: “graphs/”

Examples:

$ cadbiom_cmd solutions_search -h