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make_matrix.sh
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make_matrix.sh
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#!/bin/bash
make_matrix() {
#Make a data matrix of results for the tools just run. Salmon requires special treatment as it was run on three different modes, putting results in three different directories
if [ "$1" == "Salmon" ]; then
python ./generate.py Salmon_align `pwd` Simulation/Salmon_results/Salmon_Alignment_Results
python ./generate.py Salmon_SMEM `pwd` Simulation/Salmon_results/Salmon_SMEM_results
python ./generate.py Salmon_quasi `pwd` Simulation/Salmon_results/Salmon_quasi_results
chmod +x Salmon_align_TPM.sh
chmod +x Salmon_SMEM_TPM.sh
chmod +x Salmon_quasi_TPM.sh
./Salmon_align_TPM.sh
./Salmon_SMEM_TPM.sh
./Salmon_quasi_TPM.sh
rm Salmon_align_TPM.sh
rm Salmon_SMEM_TPM.sh
rm Salmon_quasi_TPM.sh
#Clean up to save space
#rm -r Simulation/$1"_results"
elif [ "$1" == "ground_truth" ]; then
python ./generate.py $1 `pwd` Simulation/data/simulated
chmod +x $1"_TPM.sh"
chmod +x $1"_FPKM.sh"
chmod +x $1"_Counts.sh"
./$1"_TPM.sh"
./$1"_FPKM.sh"
./$1"_Counts.sh"
rm $1"_TPM.sh"
rm $1"_FPKM.sh"
rm $1"_Counts.sh"
elif [ "$1" == "Kallisto" ] || [ "$1" == "eXpress" ] || [ "$1" == "RSEM" ] || [ "$1" == "Sailfish" ]; then
echo $1
python ./generate.py $1 `pwd` Simulation/$1"_results"
echo python ./generate.py $1 `pwd` Simulation/$1"_results"
if [ "$1" == "eXpress" ] || [ "$1" == "RSEM" ]; then
chmod +x $1"_TPM.sh"
chmod +x $1"_FPKM.sh"
chmod +x $1"_Counts.sh"
./$1"_TPM.sh"
./$1"_FPKM.sh"
./$1"_Counts.sh"
rm $1"_TPM.sh"
rm $1"_FPKM.sh"
rm $1"_Counts.sh"
else
chmod +x $1"_TPM.sh"
chmod +x $1"_Counts.sh"
./$1"_TPM.sh"
./$1"_Counts.sh"
rm $1"_TPM.sh"
rm $1"_Counts.sh"
fi
#Clean up to save space
#rm -r Simulation/$1"_results"
#If an inappropriate argument was passed, print an error message.
else
echo "Inappropriate argument passed. The following arguments are accepted: Kallisto, Salmon, eXpress and RSEM."
fi
}
"$@"