fastgenomics 1.1.0

FASTGenomics python helper

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About

This python module handles all common interfaces of your application to the FASTGenomics runtime:

• Input/Output of files

• Parameters

and provides some convenience functions.

Example:

from fastgenomics import io as fg_io

# get all parameters
parameters = fg_io.get_parameters()
...
# get a specific parameter
my_parameter = fg_io.get_parameter('my_parameter')
...
# load a file
my_input_path = fg_io.get_input_path('my_input_key')
with my_input_path.open() as f:
    # do something like f.read()
    pass

# store a file
my_output_path = fg_io.get_output_path('my_output_key')
...

Testing

If you want to test file input/output, you have to provide a sample config/input_file_mapping.json.

Testing without docker

If you want to work without docker, your paths will likely not match our default

• /app path to your app, must contain manifest.json

• /fastgenomics path to sample data. Should contain config/, data/, output/, summary/.

However, you can set them by providing environment variables FG_APP_DIR and FG_DATA_ROOT or by setting paths within your code:

from fastgenomics import io as fg_io

fg_io.set_paths('path_to/my_app', 'path_to_my/sample_data')

Keep in mind to reset the paths to default (just by not setting paths), when transforming your app into an docker-image!

For more details see our Hello Genomics Python App.