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58 lines
1.8 KiB
Python
58 lines
1.8 KiB
Python
# Last updated: Jan 2024
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# Author: Auden Cote-L'Heureux
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# This script is what users should call when running any or all components of
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# EukPhylo part 2. It briefly determines which parts of the pipeline should be
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# run (pre-Guidance, Guidance, tree building, contamination loop, and/or
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# concatenation) based on the --start and --end parameters, and then runs all
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# of these components. Each component is actually run by the run() function in
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# that component's respective script, named accordingly, which are loaded into
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# this script as Python libraries at the top.
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#!/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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#Reading in all input parameters
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params = utils.get_params()
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#First, checking for and cleaning up existing outputs from previous runs,
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#then setting up an empty output folder structure for the new run
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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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#Running pre-Guidance (preguidance.py)
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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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#Running Guidance (guidance.py)
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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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#Building trees (trees.py)
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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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#Running the contamination loop (contamination.py)
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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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#Running concatenation (concatenate.py)
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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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