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#!/usr/bin/env bash
# Runs performance tests - compares Edlib with other aligners (Parasail, Seqan, Myers).
EDLIB=~/git/edlib/build/bin/edlib-aligner
PARASAIL=~/git/parasail/apps/parasail_aligner
PARASAIL_FLAGS="-t 1 -d -e 1 -o 1 -M 0 -X 1"
# Here I am using Seqan through modified edlib aligner. It can be found in seqan-test branch of edlib repo.
SEQAN=~/git/edlib-seqan/src/aligner
MYERS=~/Dropbox/Mile/SIMD_alignment/Myers/myers_98_martin/myers
TEST_DATA=.
########################## TEST RUNNERS ########################
function edlib {
mode=$1
query=$2
target=$3
num_tests=$4
k=$5
time_sum=0
for i in $(seq $num_tests); do
sleep 1
output=$($EDLIB -m $mode -k $k $query $target)
time=$(echo "$output" | grep "Cpu time of searching" | cut -d " " -f5)
score=$(echo "$output" | grep "#0:" | cut -d " " -f2)
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $score $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Edlib:" $avg_time $score
}
function edlib_path {
mode=$1
query=$2
target=$3
num_tests=$4
time_sum=0
for i in $(seq $num_tests); do
sleep 1
output=$($EDLIB -m $mode -p -s $query $target)
time=$(echo "$output" | grep "Cpu time of searching" | cut -d " " -f5)
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Edlib (path):" $avg_time
}
function seqan {
mode=$1
query=$2
target=$3
num_tests=$4
time_sum=0
for i in $(seq $num_tests); do
sleep 1
output=$($SEQAN -m $mode -t $query $target)
time=$(echo "$output" | grep "Cpu time of searching" | cut -d " " -f5)
score=$(($(echo "$output" | grep "Seqan Score:" | cut -d " " -f4) * -1))
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $score $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Seqan:" $avg_time $score
}
function seqan_path {
mode=$1
query=$2
target=$3
num_tests=$4
time_sum=0
for i in $(seq $num_tests); do
sleep 1
output=$($SEQAN -m $mode -t -p -s $query $target)
time=$(echo "$output" | grep "Cpu time of searching" | cut -d " " -f5)
score=$(($(echo "$output" | grep "Seqan Score:" | cut -d " " -f4) * -1))
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $score $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Seqan (path):" $score $avg_time
}
function parasail {
query=$1
target=$2
num_tests=$3
time_sum=0
for i in $(seq $num_tests); do
sleep 1
output=$($PARASAIL $PARASAIL_FLAGS -a nw_striped_32 -f $target -q $query)
time=$(echo "$output" | grep "alignment time" | cut -d ":" -f2 | cut -d " " -f2)
score=$(($(head -n 1 parasail.csv | cut -d "," -f5) * -1))
rm parasail.csv
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $score $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Parasail:" $avg_time $score
}
function myers {
query=$1
target=$2
num_tests=$3
k=$4
time_sum=0
for i in $(seq $num_tests); do
sleep 1
tail -n +2 $query | tr -d '\n' > queryMyers.fasta
tail -n +2 $target | tr -d '\n' > targetMyers.fasta
output=$({ time -p $MYERS $(cat queryMyers.fasta) $k targetMyers.fasta; } 2>&1)
rm queryMyers.fasta targetMyers.fasta
time=$(echo "$output" | grep "real" | cut -d " " -f2)
time_sum=$(python -c "print($time_sum + $time)")
echo ">" "#"$i $time
done
avg_time=$(python -c "print($time_sum / $num_tests)")
echo "Myers:" $avg_time
}
############################ TESTS #############################
#Enterobacteria
echo -e "\nEnterobacteria, NW"
target=$TEST_DATA/Enterobacteria_Phage_1/Enterobacteria_phage_1.fasta
for query in $(ls $TEST_DATA/Enterobacteria_Phage_1/mutated_*_perc.fasta); do
echo $query
edlib NW $query $target 3 -1
edlib_path NW $query $target 3
seqan NW $query $target 3
seqan_path NW $query $target 3
parasail $query $target 3
done
#E coli and its illumina read, HW
echo -e "\nE coli and its illumina read, HW"
target=$TEST_DATA/E_coli_DH1/e_coli_DH1.fasta
for query in $(ls $TEST_DATA/E_coli_DH1/mason_illumina_reads/10kbp/*.fasta); do
echo $query
edlib HW $query $target 3 -1
edlib_path HW $query $target 3
seqan HW $query $target 3
# seqan_path HW $query $target 3 # Fails because it allocates too much memory.
done
#E coli and its prefix, SHW
echo -e "\nE coli and its prefix, SHW"
target=$TEST_DATA/E_coli_DH1/e_coli_DH1.fasta
for query in $(ls $TEST_DATA/E_coli_DH1/prefixes/10kbp/mutated_*_perc.fasta); do
echo $query
edlib SHW $query $target 3 -1
edlib_path SHW $query $target 3
seqan SHW $query $target 3
# seqan_path SHW $query $target 3 # Fails because it allocates too much memory.
done
#Chromosome
echo -e "\nChromosome, NW"
target=$TEST_DATA/Chromosome_2890043_3890042_0/Chromosome_2890043_3890042_0.fasta
for query in $(ls $TEST_DATA/Chromosome_2890043_3890042_0/mutated_*_perc.fasta); do
echo $query
edlib NW $query $target 3 -1
edlib_path NW $query $target 3
seqan NW $query $target 3
seqan_path NW $query $target 3
parasail $query $target 3
done
################### Myers #####################
echo -e "\nMyers"
target=$TEST_DATA/E_coli_DH1/e_coli_DH1.fasta
k=100
for query_file in e_coli_DH1_illumina_1x10000.fasta; do
query=$TEST_DATA/E_coli_DH1/mason_illumina_reads/10kbp/$query_file
echo $query $k
edlib HW $query $target 3 $k
myers $query $target 3 $k
done
k=1000
for query_file in e_coli_DH1_illumina_1x10000.fasta mutated_97_perc.fasta mutated_94_perc.fasta mutated_90_perc.fasta; do
query=$TEST_DATA/E_coli_DH1/mason_illumina_reads/10kbp/$query_file
echo $query $k
edlib HW $query $target 3 $k
myers $query $target 3 $k
done
k=10000
for query in $(ls $TEST_DATA/E_coli_DH1/mason_illumina_reads/10kbp/*); do
echo $query $k
edlib HW $query $target 3 $k
myers $query $target 3 $k
done
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