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35 lines
843 B
Python
35 lines
843 B
Python
#!/usr/bin/python3
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import os, sys, re
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import utils
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import preguidance
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import guidance
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import trees
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from logger import Logger
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if __name__ == '__main__':
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params = utils.get_params()
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Logger.Message('Cleaning up existing files and organizing output folder', Logger.BOLD)
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utils.clean_up(params)
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if params.start == 'raw':
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Logger.Message('Running preguidance', Logger.BOLD)
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preguidance.run(params)
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if params.start in ('unaligned', 'raw') and params.end in ('aligned', 'trees'):
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Logger.Message('Running guidance', Logger.BOLD)
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guidance.run(params)
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if params.end == 'trees':
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Logger.Message('Building trees', Logger.BOLD)
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trees.run(params)
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if params.contamination_loop != None:
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Logger.Message('Running contamination loop', Logger.BOLD)
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#if not params.keep_temp:
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# os.system('rm -r ' + params.output + '/Output/Temp')
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