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Update contamination.py

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Godwin N. Ani 2025-04-04 15:28:08 -04:00 committed by GitHub
parent d161957d86
commit 0cfea8840c
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1 changed files with 25 additions and 7 deletions
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PTL2/Scripts/contamination.py
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@ -327,11 +327,22 @@ def cl_mafft(params):
#Utility function to run FastTree in between iterations (if this is the chosen tree-building method)
def cl_fasttree(params):
for file in os.listdir(params.output + '/Output/Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('FastTree ' + params.output + '/Output/Guidance/' + file + ' > ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.FastTree.tre')
#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'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --prefix ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.IQTree.tre')
#Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method)
def cl_iqtree_fast(params):
for file in os.listdir(params.output + '/Output/Guidance'):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('iqtree2 -s ' + params.output + '/Output/Guidance/' + file + ' -m LG+G -T 10 --fast --prefix ' + params.output + '/Output/Trees/' + file.split('.')[0] + '.IQTree.tre')
#Wrapper script to manage parameters and iteration
def run(params):
@ -440,11 +451,18 @@ def run(params):
if params.cl_tree_method == 'fasttree':
cl_fasttree(params)
else:
if 'iqtree' in params.cl_tree_method:
os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*')
elif params.cl_tree_method == 'raxml':
os.system('rm -r ' + params.output + '/Output/Intermediate/RAxML/*')
elif params.cl_tree_method == 'iqtree':
cl_iqtree(params)
elif params.cl_tree_method == 'iqtree_fast':
cl_iqtree_fast(params)
elif params.cl_tree_method == 'raxml':
os.system('rm -r ' + params.output + '/Output/Intermediate/RAxML/*')
trees.run(params)
trees.run(params)
#if 'iqtree' in params.cl_tree_method:
#os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*')
#elif params.cl_tree_method == 'raxml':
#os.system('rm -r ' + params.output + '/Output/Intermediate/RAxML/*')
#trees.run(params)