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adding contamination loop back to wrapper

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Auden Cote-L'Heureux 2024-02-07 11:31:03 -05:00 committed by GitHub
parent 0f2ae76d13
commit 877aabd2ef
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1 changed files with 5 additions and 0 deletions
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PTL2/Scripts/phylotol.py
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@ -1,5 +1,6 @@
#!/usr/bin/python3
import os, sys, re
import contamination
import utils
import preguidance
import guidance
@ -27,6 +28,10 @@ if __name__ == '__main__':
print('\nBuilding trees\n')
trees.run(params)
if params.contamination_loop != None:
print('\nRunning contamination loop\n')
contamination.run(params)
if params.concatenate:
print('\nChoosing orthologs and concatenating alignments...\n')
concatenate.run(params)