bionetgen.core package

Submodules

bionetgen.core.defaults module

class bionetgen.core.defaults.BNGDefaults[source]

Bases: object

bionetgen.core.defaults.get_latest_bng_version()[source]

bionetgen.core.exc module

exception bionetgen.core.exc.BioNetGenError[source]

Bases: Exception

Generic errors.

bionetgen.core.main module

bionetgen.core.main.graphDiff(config, args)[source]
bionetgen.core.main.plotDAT(inp, out='.', kw={})[source]

Convenience function to plot dat/scan files from the CLI

Usage: plotDAT(inp, out, kw)

inpstr

input gdat/cdat/scan file to plot

outstr

(optional) output file path, can be used to define the output format as well. Default is the current folder, filename is the same as the input file and default format is PNG.

kwdict

(optional) this is a set of keyword arguments you want to pass for certain matplotlib options. Check -h for details

bionetgen.core.main.printInfo(config, args)[source]

Uses BNGInfo class to print BioNetGen information using arguments and config from Cement framework.

bionetgen.core.main.runAtomizeTool(config, args)[source]
bionetgen.core.main.runCLI(config, args)[source]

Convenience function to run BNG2.pl from the CLI app

Usage: runCLI(config, args)

configdict

configuration dictionary from BioNetGen cement app

argsargparse.Namespace

arguments parsed from the command line with argparser.

bionetgen.core.main.visualizeModel(config, args)[source]

Uses BNGVisualize class to visualize BNGL models using arguments and configuration from Cement framework.

bionetgen.core.notebook module

class bionetgen.core.notebook.BNGNotebook(nb_template, **kwargs)[source]

Bases: object

This is a class for writing BNG notebook from a template and given arguments.

Initalize with keywords to replace values in the template. E.g. BNGNotebook(template_file, TEST=”CHANGE”).write(outfile) will write the template file to outfile while changing every instance of “TEST” to “CHANGE”

templatestr

the notebook template to use

odictdict

the dictionary built from keywords the class is initalized with

write(outfile)

writes the template file to outfile, replacing keywords

write(outfile)[source]

This method will overwrite the given arguments

bionetgen.core.plot module

bionetgen.core.result module

bionetgen.core.version module

bionetgen.core.version.get_version(version=(0, 6, 0, 'alpha', 0))[source]

Module contents