From 8c7a1a2eed09b5af20b721d2535ee3f6469549e8 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Mon, 7 Apr 2025 11:29:15 -0400 Subject: [PATCH] Update contamination.py --- PTL2/Scripts/contamination.py | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/PTL2/Scripts/contamination.py b/PTL2/Scripts/contamination.py index dff9172..10608bf 100644 --- a/PTL2/Scripts/contamination.py +++ b/PTL2/Scripts/contamination.py @@ -334,12 +334,12 @@ def cl_fasttree(params): #Utility function to run Iqtree in between iterations (if this is the chosen tree-building method) def cl_iqtree(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'): if file.split('.')[-1] in ('fasta', 'fas', 'faa'): + 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) 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'): @@ -348,17 +348,18 @@ def cl_iqtree(params): #Utility function to run Iqtree_fast in between iterations (if this is the chosen tree-building method) 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'): 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') + 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) + 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') + #Wrapper script to manage parameters and iteration def run(params):