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Update contamination.py

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Godwin N. Ani 2025-04-07 11:54:36 -04:00 committed by GitHub
parent 8c7a1a2eed
commit fba84adb17
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1 changed files with 6 additions and 6 deletions
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PTL2/Scripts/contamination.py
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@ -341,9 +341,9 @@ def cl_iqtree(params):
tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_iqtree_outdir)
os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')
#Copy over the final output
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')
#Copy over the final output
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')
#Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method)
@ -355,9 +355,9 @@ def cl_iqtree_fast(params):
tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_iqtree_outdir)
os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --prefix --fast ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')
#Copy over the final output
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')
#Copy over the final output
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')
#Wrapper script to manage parameters and iteration