Command line usage

Cadbiom - Command Line Interface

usage: cadbiom_cmd [-h] [-vv [VERBOSE]]
                   {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”

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_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