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Contents
#!/bin/bash set -e set -x # Hierarchical OTU clustering # Austin G. Davis-Richardson # <harekrishna at gmail dot com> # http://github.com/audy/lederhosen reads='sorted.fasta' out='h_clustering' mkdir -p $out # initial clustering at 80% lederhosen cluster --input=$reads --output=$out/clusters_0.80.uc --identity=0.80 # filter UC file lederhosen uc_filter --input=$out/clusters_0.80.uc --output=$out/clusters_0.80.uc.filtered --reads=1 --samples=1 # get reads for each cluster mkdir -p $out/split_80 lederhosen split --clusters=$out/clusters_0.80.uc.filtered --reads=$reads --out-dir=$out/split_80/ # now cluster each of those at 90% for fasta in $out/split_80/*.fasta do # sort (awww, do I really have to do this again?) lederhosen sort --input=$fasta --output=$fasta.sorted # cluster lederhosen cluster --input=$fasta.sorted --output=$fasta.uc --identity=0.90 # split split=$out/split_80.90_$(basename $fasta .fasta) lederhosen split --clusters=$fasta.uc --reads=$fasta --out-dir=$split done # Do it again at 95% for fasta in $out/split_80/split_*_90.fasta/*.fasta do # cluster lederhosen cluster --input=$fasta --output=$fasta.uc --identity=90 # split split=$outdir/80.90.$fasta.fasta mkdir -p $split lederhosen split --clusters=$fasta.uc --reads=$input --out-dir=$split done
Version data entries
37 entries across 37 versions & 1 rubygems