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Update contamination.py

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Godwin N. Ani 2025-04-07 11:20:34 -04:00 committed by GitHub
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commit e8aa277e44
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1 changed files with 21 additions and 18 deletions
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PTL2/Scripts/contamination.py
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@ -332,26 +332,29 @@ def cl_fasttree(params):
os.system('FastTree ' + params.output + '/Output/Guidance/' + file + ' > ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.FastTree.tre') os.system('FastTree ' + params.output + '/Output/Guidance/' + file + ' > ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.FastTree.tre')
#Run IQ-Tree #Utility function to run Iqtree in between iterations (if this is the chosen tree-building method)
if params.cl_tree_method == 'iqtree' or params.cl_tree_method == 'iqtree_fast': def cl_iqtree(params):
#Make intermediate folders
if not os.path.isdir(params.output + '/Output/Intermediate/IQTree'): if not os.path.isdir(params.output + '/Output/Intermediate/IQTree'):
os.mkdir(params.output + '/Output/Intermediate/IQTree') os.mkdir(params.output + '/Output/Intermediate/IQTree')
tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0] tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_iqtree_outdir) os.mkdir(tax_iqtree_outdir)
#Utility function to run Iqtree in between iterations (if this is the chosen tree-building method)
def cl_iqtree(params):
for file in os.listdir(params.output + '/Output/Guidance'): for file in os.listdir(params.output + '/Output/Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'): if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
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') 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')
#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)
def cl_iqtree_fast(params): def cl_iqtree_fast(params):
if not os.path.isdir(params.output + '/Output/Intermediate/IQTree'):
os.mkdir(params.output + '/Output/Intermediate/IQTree')
tax_iqtree_outdir = params.output + '/Output/Intermediate/IQTree/' + file.split('.')[0].split('_preguidance')[0]
os.mkdir(tax_iqtree_outdir)
for file in os.listdir(params.output + '/Output/Guidance'): for file in os.listdir(params.output + '/Output/Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'): if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --fast --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree') os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --fast --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree')
#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')