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#!/bin/bash
nodes=4 #no. of cluster nodes to use
file=$1; #first argument name of dat file
defaultPrimer="ATTAGATACCC[ACTG]GGTAG"
primer=${2:-$defaultPrimer}
echo $file
stub=${file%.dat}
echo "Calculating .fdist file"
mpirun $mpiextra -np $nodes PyroDist -in $file -out ${stub} > ${stub}.fout
echo "Clustering .fdist file"
FCluster -in ${stub}.fdist -out ${stub}_X > ${stub}.fout
rm ${stub}.fdist
rm ${stub}_X.otu ${stub}_X.tree
echo "Running PyroNoise"
mpirun $mpiextra -np $nodes PyroNoiseM -din ${file} -out ${stub}_s60_c01 -lin ${stub}_X.list -s 60.0 -c 0.01 > ${stub}_s60_c01.pout
Truncate.pl 220 < ${stub}_s60_c01_cd.fa > ${stub}_s60_c01_T220.fa
echo "Running SeqDist"
mpirun $mpiextra -np $nodes SeqDist -in ${stub}_s60_c01_T220.fa > ${stub}_s60_c01_T220.seqdist
FCluster -in ${stub}_s60_c01_T220.seqdist -out ${stub}_s60_c01_T220_S > ${stub}_s60_c01_T220.fcout
echo "Running SeqNoise"
mpirun $mpiextra -np $nodes SeqNoise -in ${stub}_s60_c01_T220.fa -din ${stub}_s60_c01_T220.seqdist -lin ${stub}_s60_c01_T220_S.list -out ${stub}_s60_c01_T220_s30_c08 -s 30.0 -c 0.08 -min ${stub}_s60_c01.mapping > ${stub}_s60_c01_T220.snout
rm ${stub}_s60_c01_T220_S.otu ${stub}_s60_c01_T220_S.tree ${stub}_s60_c01_T220.seqdist
echo "Remove degenerate primers"
sed 's/^${primer}//' ${stub}_s60_c01_T220_s30_c08_cd.fa > ${stub}_s60_c01_T220_s30_c08_P.fa
echo "Clustering OTUs"
mpirun $mpiextra -np $nodes NDist -i -in ${stub}_s60_c01_T220_s30_c08_P.fa > ${stub}_s60_c01_T220_s30_c08_P.ndist
FCluster -i -in ${stub}_s60_c01_T220_s30_c08_P.ndist -out ${stub}_s60_c01_T220_s30_c08_P > ${stub}_s60_c01_T220_s30_c08_P.fcout
rm ${stub}_s60_c01_T220_s30_c08_P.ndist
echo "Removing intermediate files"
rm *out
exit 0
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