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Adding trimal cutoff as parameter

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Auden Cote-L'Heureux 2025-01-09 12:11:54 -05:00 committed by GitHub
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commit 733851b957
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PTL2/Scripts/contamination.py
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@ -323,7 +323,7 @@ def cl_mafft(params):
if file.split('.')[-1] in ('fasta', 'fas', 'faa'): if file.split('.')[-1] in ('fasta', 'fas', 'faa'):
os.system('mafft ' + params.output + '/Output/Pre-Guidance/' + file + ' > ' + params.output + '/Output/NotGapTrimmed/' + file) os.system('mafft ' + params.output + '/Output/Pre-Guidance/' + file + ' > ' + params.output + '/Output/NotGapTrimmed/' + file)
os.system('Scripts/trimal-trimAl/source/trimal -in ' + params.output + '/Output/NotGapTrimmed/' + file + ' -out ' + params.output + '/Output/Guidance/' + file.split('.')[0] + '.95gapTrimmed.fasta' + ' -gapthreshold 0.05 -fasta') os.system('Scripts/trimal-trimAl/source/trimal -in ' + params.output + '/Output/NotGapTrimmed/' + file + ' -out ' + params.output + '/Output/Guidance/' + file.split('.')[0] + '.95gapTrimmed.fasta' + ' -gapthreshold ' + str(params.trimal_cutoff) + ' -fasta')
#Utility function to run FastTree in between iterations (if this is the chosen tree-building method) #Utility function to run FastTree in between iterations (if this is the chosen tree-building method)
def cl_fasttree(params): def cl_fasttree(params):