snake-flu / datafunk

Miscellaneous data manipulation tools

datafunk

Miscellaneous data manipulation tools

Install

Either pip install using command

pip install .

or use

python setup.py install

and test with

python setup.py test

Adding functions to this suite

Ideally the function name should be used as the filename and the argparse group. In the following example, the function name is remove_dat_junk.

1. Add your script to directory datafunk e.g. datafunk/remove_dat_junk.py
2. Update datafunk/__init__.py and datafunk/subcommands/__init__.py by adding the command name to the all lists
3. Add a new command line parameter section to datafunk/__main__.py This should start by defining a new argparse group, e.g.

subparser_remove_dat_junk = subparsers.add_parser(
        "remove_dat_junk",
        usage="datafunk remove_dat_junk -i <input>",
        help="Example command",
    )

then include all the arguments, e.g.

    subparser_remove_dat_junk.add_argument(
        "-i",
        "--input_file",
        dest="input_file",
        action="store",
        type=str,
        help="Input file: something about the input file format",
    )

and end with the entry point

    subparser_remove_dat_junk.set_defaults(func=datafunk.subcommands.remove_dat_junk.run)

4. Create file datafunk/subcommands/remove_dat_junk.py which defines how to run given the command line parameters. Alternatively, specify the entrypoint within the main script file.
5. If you have tests, add the test data to a subdirectory e.g. tests/data/remove_dat_junk, and add the test file tests/remove_dat_junk_test.py. This file should contain unit tests which have names test_* and ideally be informative about which function they test/the result.
6. If the script has any new dependencies, update install_requires section of setup.py - this means that it can be pip installed from a conda environment file without a hitch.

Function List

   - clean_names
   - merge_fasta
   - remove_fasta 
   - filter_low_coverage
   - process_gisaid_data
   - sam_2_fasta
   - phylotype_consensus