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README.md

README.md

modify/make demo

Get this repo.

  1. git clone git@github.com:uc-cdis/planx-bioinfo-tools.git
  2. cd planx-bioinfo-tools/

Checkout this branch.

  1. git checkout feat/auto_tools

Move to the directory containing the modify.py and make.py modules.

  1. cd dictionary_tools/code/modify

Run this command:

  1. python modify.py -p input/dictionaries/example_dictionary -i examples -n demo_namespace -o demo

View modify results in output/modify

Notes on usage:

  • -p/--path_to_schemas: Optional. Path to input schemas, relative to directory dictionary_tools/.
  • -i/--input_tsv: Required. Name of directory containing target nodes and variables TSV files.
  • -n/--namespace: Required. Desired namespace for the output dictionary - e.g., niaid.bionimbus.org.
  • -o/--out_dict_name: Optional. Name of output dictionary.

compare demo

After running the above demo, move to directory code/compare and run this command:

  1. python compare.py -a input/dictionaries/example_dictionary -b output/modify/demo -o demo

View comparison results in output/compare

Notes on usage:

  • -a: Required. Path to one set of dictionary files, relative to directory dictionary_tools/.
  • -b: Required. Path to the other set of dictionary files, relative to directory dictionary_tools/.
  • -o: Optional. Name of output summary JSON file.

get_tsv demo

Move to directory code/get_tsv and run this command:

  1. python get_tsv.py -p input/dictionaries/example_dictionary -o demo

View get_tsv results in output/get_tsv

Notes on usage:

  • -p/--path_to_schemas: Required. Path to the target set of dictionary files, relative to directory dictionary_tools/.
  • -o/--out_dir_name: Optional. Name of output directory.
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