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palmerito0 edited this page Dec 17, 2021 · 4 revisions

extract_modules.py

extract_modules.py is a standalone script that will extract reactions and contingencies from a rxncon Excel file based on their Quality and Module tags. These tags should be present as additional columns in the rxncon excel file. This script automatically adds any reactions necessary for the request module to compile into a valid rxncon system

Running

Run extract_modules.py using python3 extract_modules.py --<parameter> <value>

Parameters

  • file: Name of input Excel file. [required]
  • output: Name of output Excel file. Default: modules.xlsx
  • modules: Comma-separated list of modules to be extracted from input file. Put quotes around this when running from the commandline (ie --modules "module1,module2"
  • quality: Minimum quality for a rxncon rules to be kept. Default: 0. (Note: currently, modules that do not have a quality assigned to them will be ignored.

Auto-generated help

Usage: extract_modules.py [OPTIONS]

Options:
  --file TEXT          Name of input file.  [required]
  --output TEXT        Name of output file. Default: modules.xlsx
  --modules TEXT       Comma-separated list of modules to be extracted from
                       input file.
  --quality INTEGER    Minimum quality of rules to be kept. Default: 0
  -v, --verbosity LVL  Either CRITICAL, ERROR, WARNING, INFO or DEBUG
  --help               Show this message and exit.
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