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Fixing underscore/dot issue in trees.py

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Auden Cote-L'Heureux 2024-04-15 16:25:32 -04:00 committed by GitHub
parent a1d92144e4
commit 18f4686223
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1 changed files with 4 additions and 4 deletions
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PTL2/Scripts/trees.py
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@ -46,9 +46,9 @@ def run(params):
os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T AUTO --prefix ' + tax_iqtree_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree') os.system('iqtree2 -s ' + guidance_path + '/' + file + ' -m LG+G -T AUTO --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')
#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.tree') #color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.tree')
else: else:
print('\nWARNING: No tree file created by IQ-Tree for OG ' + file[:10] + '\n') print('\nWARNING: No tree file created by IQ-Tree for OG ' + file[:10] + '\n')
@ -68,7 +68,7 @@ def run(params):
os.system('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads)) os.system('raxmlHPC -s ' + tax_raxml_outdir + '/aligned.phy -m PROTGAMMALG -f d -p 12345 -# 10 -n ' + file.split('.')[0].split('_preguidance')[0] + '_RAxML -T ' + str(params.guidance_threads))
#Copy over final output #Copy over final output
if os.path.isfile(tax_raxml_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '_IQTree.treefile'): if os.path.isfile(tax_raxml_outdir + '/' + file.split('.')[0].split('_preguidance')[0] + '.IQTree.treefile'):
os.system('cp ' + tax_raxml_outdir + '/RAxML_bestTree.' + file.split('.')[0].split('_preguidance')[0] + '_RAxML ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree') os.system('cp ' + tax_raxml_outdir + '/RAxML_bestTree.' + file.split('.')[0].split('_preguidance')[0] + '_RAxML ' + params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
#color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree') #color(params.output + '/Output/Trees/' + file.split('.')[0].split('_preguidance')[0] + '_RAxML.tree')
else: else: