Source code for bionetgen.core.main

import subprocess, os
from bionetgen.core.tools import BNGInfo
from bionetgen.core.tools import BNGVisualize
from bionetgen.core.tools import BNGCLI
from bionetgen.core.tools import BNGGdiff
from bionetgen.core.notebook import BNGNotebook
from bionetgen.core.utils.utils import run_command

import os, sys


# TODO Consolidate how config is being accessed. It's
# almost like each function accesses the configs from
# a different path
[docs]def runCLI(app): """ Convenience function to run BNG2.pl from the CLI app Usage: runCLI(config, args) Arguments --------- config : dict configuration dictionary from BioNetGen cement app args : argparse.Namespace arguments parsed from the command line with argparser. """ args = app.pargs config = app.config # this pulls out the arguments sys.tracebacklimit = args.traceback_depth inp_file = args.input output = args.output log_file = args.log_file # if you set args.bngpath it should take precedence app.log.debug("Pulling BNG path from config", f"{__file__} : runCLI()") config_bngpath = config.get("bionetgen", "bngpath") # and instantiates the CLI object app.log.debug("Instantiating BNGCLI object", f"{__file__} : runCLI()") cli = BNGCLI(inp_file, output, config_bngpath, log_file=log_file, app=app) cli.stdout = config.get("bionetgen", "stdout") cli.stderr = config.get("bionetgen", "stderr") app.log.debug("Running", f"{__file__} : runCLI()") cli.run()
[docs]def plotDAT(app): """ Convenience function to plot dat/scan files from the CLI Usage: plotDAT(inp, out, kw) Arguments --------- inp : str input gdat/cdat/scan file to plot out : str (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. kw : dict (optional) this is a set of keyword arguments you want to pass for certain matplotlib options. Check -h for details """ args = app.pargs # we need to have gdat/cdat files # TODO: Transition to BNGErrors and logging assert ( args.input.endswith(".gdat") or args.input.endswith(".cdat") or args.input.endswith(".scan") ), "Input file has to be either a gdat or a cdat file" inp = args.input out = args.output kw = dict(args._get_kwargs()) # if we want to plot directly into the folder # we are in we need to get the path correctly if out == ".": path, fname = os.path.split(inp) fnoext, ext = os.path.splitext(fname) out = os.path.join(path, "{}.png".format(fnoext)) # use the plotter object to get the plot from bionetgen.core.tools import BNGPlotter app.log.debug("Instantiating BNGPlotter object", f"{__file__} : plotDAT()") plotter = BNGPlotter(inp, out, app=app, **kw) app.log.debug("Plotting", f"{__file__} : plotDAT()") plotter.plot()
[docs]def runAtomizeTool(app): # pull args/config args = app.pargs config = app.config # run AtomizeTool from bionetgen.atomizer import AtomizeTool app.log.debug("Instantiating AtomizeTool object", f"{__file__} : runAtomizeTool()") a = AtomizeTool(parser_namespace=args, app=app) # do config specific stuff here if need be, or remove the config requirement app.log.debug("Atomizing", f"{__file__} : runAtomizeTool()") a.run()
[docs]def printInfo(app): """ Uses BNGInfo class to print BioNetGen information using arguments and config from Cement framework. """ config = app.config app.log.debug("Instantiating BNGInfo object", f"{__file__} : printInfo()") info = BNGInfo(config=config, app=app) app.log.debug("Gathering and printing info", f"{__file__} : printInfo()") info.gatherInfo() info.messageGeneration() info.run()
[docs]def visualizeModel(app): """ Uses BNGVisualize class to visualize BNGL models using arguments and configuration from Cement framework. """ # pull args/config from app args = app.pargs config = app.config # pull relevant arguments for the tool inp = args.input out = args.output vtype = args.type app.log.debug("Pulling BNG path from config", f"{__file__} : visualizeModel()") # if you set args.bngpath it should take precedence config_bngpath = config.get("bionetgen", "bngpath") # run visualize tool app.log.debug("Instantiating BNGVisualize object", f"{__file__} : visualizeModel()") viz = BNGVisualize(inp, output=out, vtype=vtype, bngpath=config_bngpath, app=app) app.log.debug("Visualizing", f"{__file__} : visualizeModel()") viz.run()
[docs]def graphDiff(app): # pull args and config for the tool args = app.pargs # if you set args.bngpath it should take precedence app.log.debug("Instantiating BNGGdiff object", f"{__file__} : graphDiff()") gdiff = BNGGdiff( args.input, args.input2, out=args.output, out2=args.output2, mode=args.mode, colors=args.colors, app=app, ) app.log.debug("Calculating graph diff", f"{__file__} : graphDiff()") gdiff.run()
[docs]def generate_notebook(app): args = app.pargs if args.input is not None: # we want to use the template to write a custom notebok # TODO: Transition to BNGErrors and logging assert args.input.endswith( ".bngl" ), f"File {args.input} doesn't have bngl extension!" try: app.log.debug("Loading model", f"{__file__} : notebook()") import bionetgen m = bionetgen.bngmodel(args.input) str(m) except: app.log.error("Failed to load model", f"{__file__} : notebook()") raise RuntimeError(f"Couldn't import given model: {args.input}!") notebook = BNGNotebook( app.config["bionetgen"]["notebook"]["template"], INPUT_ARG=args.input, ) else: # just use the basic notebook notebook = BNGNotebook(app.config["bionetgen"]["notebook"]["path"]) # find our file name if len(args.output) == 0: fname = app.config["bionetgen"]["notebook"]["name"] else: fname = args.output # write the notebook out if os.path.isdir(fname): if args.input is not None: basename = os.path.basename(args.input) mname = basename.replace(".bngl", "") fname = mname + ".ipynb" else: mname = app.config["bionetgen"]["notebook"]["name"] fname = os.path.join(args.output, mname) app.log.debug(f"Writing notebook to file: {fname}", f"{__file__} : notebook()") notebook.write(fname) # open the notebook with nbopen # TODO: deal with stdout/err app.log.debug( f"Attempting to open notebook {fname} with nbopen", f"{__file__} : notebook()", ) stdout = getattr(subprocess, app.config["bionetgen"]["stdout"]) stderr = getattr(subprocess, app.config["bionetgen"]["stderr"]) if args.open: command = ["nbopen", fname] rc, _ = run_command(command)