python_example.py

"""
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The Synthego ICE software was developed at Synthego Corporation.

Permission to use, copy, modify and distribute any part of Synthego ICE for
educational, research and non-profit purposes, without fee, and without a
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this paragraph and the following paragraphs appear in all copies.

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indirect, special, incidental, or consequential damages, including lost
profits, arising out of the use of Synthego ICE, even if Synthego Corporation
has been advised of the possibility of such damage.

The Synthego ICE tool provided herein is on an "as is" basis, and the Synthego
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enhancements, or modifications. The Synthego Corporation makes no
representations and extends no warranties of any kind, either implied or
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"""


import os
from pprint import pprint as pp

from ice.analysis import single_sanger_analysis, multiple_sanger_analysis

# Running a single analysis

control_path = os.path.abspath('./ice/tests/test_data/good_example_control.ab1')
sample_path = os.path.abspath('./ice/tests/test_data/good_example_edited.ab1')
guide = 'AACCAGTTGCAGGCGCCCCA'
base_outputname = './results/good_example'
donor = None
verbose = True

results = single_sanger_analysis(control_path=control_path,
                                 sample_path=sample_path,
                                 base_outputname=base_outputname,
                                 guide=guide,
                                 donor=donor,
                                 verbose=verbose)

pp(results)


# Running a batch analysis

definition_file = os.path.abspath('./ice/tests/test_data/batch_example.xlsx')
data_directory = os.path.abspath('./ice/tests/test_data/')
output_dir = './results/batch_example'

job_args = (definition_file, output_dir)
job_kwargs = {
    'verbose': True,
    'data_dir': data_directory
}

multiple_sanger_analysis(*job_args, **job_kwargs)