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39 lines
916 B
Python
39 lines
916 B
Python
#!/usr/bin/python3
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import os, sys, re
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import contamination
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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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import concatenate
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if __name__ == '__main__':
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params = utils.get_params()
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if not (params.concatenate and params.start == 'trees'):
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print('\nCleaning up existing files and organizing output folder\n')
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utils.clean_up(params)
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if params.start == 'raw':
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print('\nRunning preguidance\n')
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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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print('\nRunning guidance\n')
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guidance.run(params)
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if params.start != 'trees' and params.end == 'trees':
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print('\nBuilding trees\n')
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trees.run(params)
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if params.contamination_loop != None:
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print('\nRunning contamination loop\n')
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contamination.run(params)
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if params.concatenate:
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print('\nChoosing orthologs and concatenating alignments...\n')
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concatenate.run(params)
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