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Changed progressive_clustering to be compatible with new usearch8.0.1517 #79

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Changed progressive_clustering to be compatible with new usearch8.0.1517 #79

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5726b74
Changed progressive_clustering to be compatible with new usearch8.0.1517
Jan 26, 2015
2a1d383
Revert back to almlab smiletrain; moved USEARCH changes to branch USE…
Mar 21, 2017
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10 changes: 5 additions & 5 deletions otu_caller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -531,17 +531,17 @@ def dbotu_progressive_clustering(self):
cmds = []
cmds.append(['perl', '%s/find_replace_seq_dash-period.pl' % perllib, 'unique.good.align', 'unique.good.align.ng'])
cmds.append(['perl', '%s/fasta2uchime_size.pl' % perllib, 'unique.f0.good.mat', 'unique.good.align.ng', 'unique.good.align.ng.size'])
cmds.append([self.usearch, '-cluster_otus', 'unique.good.align.ng.size', '--uc', 'unique.97.uc', '-otus', 'unique.97.otus.fa', '-fastaout', 'unique.97.fastaout.fa'])
cmds.append(['perl', '%s/USEARCH_fastaout2list.pl' % perllib, 'unique.97.fastaout.fa', 'unique.97.uc.list'])
cmds.append([self.usearch, '-sortbylength', 'unique.97.otus.fa', '-output', 'unique.97.sorted.fa'])
cmds.append([self.usearch, '-cluster_otus', 'unique.good.align.ng.size', '-uparseout', 'unique.97.uc', '-otus', 'unique.97.otus.fa'])
cmds.append(['perl', '%s/UC2list4.pl' % perllib, 'unique.97.uc', 'unique.97.uc.list'])
cmds.append([self.usearch, '-sortbylength', 'unique.97.otus.fa', '-fastaout', 'unique.97.sorted.fa'])
uc_list=['unique.97.uc.list']
upper=96
lower=int(100*(1-self.dbotu_id)) - 1
for i in range(upper, lower, -1):
previous= i + 1
cmds.append([self.usearch, '-cluster_smallmem', 'unique.%d.sorted.fa' % previous, '-id', '0.%d' % i, '--uc', 'unique.%d.uc' % i, '-centroids', 'unique.%d.otus.fa' % i])
cmds.append(['perl', '%s/UC2list3.pl' % perllib, 'unique.%d.uc' % i, 'unique.%d.uc.list' % i])
cmds.append([self.usearch, '-sortbylength', 'unique.%d.otus.fa' % i, '-output', 'unique.%d.sorted.fa' % i])
cmds.append([self.usearch, '-sortbylength', 'unique.%d.otus.fa' % i, '-fastaout', 'unique.%d.sorted.fa' % i])
uc_list.append(str('unique.%d.uc.list' % i))
input_lists=",".join([str(x) for x in uc_list])
cmds.append(['perl', '%s/merge_progressive_clustering4.pl'% perllib, input_lists, 'unique.PC.final.list'])
Expand Down Expand Up @@ -569,7 +569,7 @@ def dbotu_remove_chimeras(self):
cmds = []
cmd = 'perl %s/fasta2filter_from_mat_SmileTrain.pl unique.dbOTU.mat q.derep.fst > unique.dbOTU.ng.fasta' % perllib
cmds.append(cmd)
cmd = '%s -uchime_denovo unique.dbOTU.ng.fasta -nonchimeras unique.dbOTU.nonchimera.fasta -strand plus' % self.usearch
cmd = '%s -uchime_denovo unique.dbOTU.ng.fasta -nonchimeras unique.dbOTU.nonchimera.fasta' % self.usearch
cmds.append(cmd)
cmd = 'perl %s/filter_mat_from_fasta_SmileTrain.pl unique.dbOTU.mat unique.dbOTU.nonchimera.fasta > unique.dbOTU.nonchimera.mat' % perllib
cmds.append(cmd)
Expand Down