From 7074a1e71a959b6db92f4003cdb8d638718df971 Mon Sep 17 00:00:00 2001 From: "Godwin N. Ani" Date: Mon, 7 Apr 2025 12:24:56 -0400 Subject: [PATCH] Update contamination.py --- PTL2/Scripts/contamination.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/PTL2/Scripts/contamination.py b/PTL2/Scripts/contamination.py index b6162fd..eb6bbc5 100644 --- a/PTL2/Scripts/contamination.py +++ b/PTL2/Scripts/contamination.py @@ -344,6 +344,7 @@ def cl_iqtree(params): #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') + 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) @@ -358,6 +359,7 @@ def cl_iqtree_fast(params): #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') + os.system('rm -r ' + params.output + '/Output/Intermediate/IQTree/*') #Wrapper script to manage parameters and iteration