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Update contamination.py

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Godwin N. Ani 2025-04-07 12:24:56 -04:00 committed by GitHub
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commit 7074a1e71a
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PTL2/Scripts/contamination.py
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@ -344,6 +344,7 @@ def cl_iqtree(params):
#Copy over the final output #Copy over the final output
if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'): if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree') os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*')
#Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method) #Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method)
@ -358,6 +359,7 @@ def cl_iqtree_fast(params):
#Copy over the final output #Copy over the final output
if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'): if os.path.isfile(tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree') os.system('cp ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*')
#Wrapper script to manage parameters and iteration #Wrapper script to manage parameters and iteration