perf_tests2.sh

#!/usr/bin/env bash

# Runs performance tests.
# Here we run Edlib with different sizes of queries, with special focus on short queries,
# since that is where Edlib needs to improve.

EDLIB=~/git/edlib/build/bin/edlib-aligner

TEST_DATA=.

########################## TEST RUNNERS ########################

F_YELLOW='\e[93m'
F_NONE='\e[0m'
F_UNDERLINE='\e[4m'
F_NO_UNDERLINE='\e[24m'
F_BOLD='\e[1m'
F_NO_BOLD='\e[21m'

function echo_underlined {
    local input=$1
    echo -e "${F_UNDERLINE}${input}${F_NO_UNDERLINE}"
}

function echo_bolded {
    local input=$1
    echo -e "${F_BOLD}${input}${F_NO_BOLD}"
}

function edlib {
    mode=$1
    query=$2
    target=$3
    num_tests=$4
    k=$5
    r=${6-1}  # Number of repetitions, default is 1.

    time_sum=0
    for i in $(seq $num_tests); do
        sleep 0.25
        output=$($EDLIB -m $mode -k $k -r $r $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 -e "    => Edlib, $r repetition(s): time=${F_YELLOW}${avg_time}${F_NONE}s, score=$score"
}

function edlib_path {
    mode=$1
    query=$2
    target=$3
    num_tests=$4
    r=${5-1}  # Number of repetitions, default is 1.

    time_sum=0
    for i in $(seq $num_tests); do
        sleep 0.1
        output=$($EDLIB -m $mode -r $r -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 -e "    => Edlib (path), $r repetition(s): time=${F_YELLOW}${avg_time}${F_NONE}s, score=$score"
}


############################ TESTS #############################



# ---------------------- Short reads ----------------------- #

# SHW (prefix).
echo_bolded "\nSHW, short query (<= 500bp) and long target."
target=$TEST_DATA/E_coli_DH1/e_coli_DH1.fasta
for query_length in 50 100 250 500; do
    echo_underlined "Query length: $query_length"
    for query in $(ls $TEST_DATA/E_coli_DH1/prefixes/${query_length}bp/mutated_*_perc.fasta); do
        echo "  Query: $query"
        edlib      SHW $query $target 3 -1 100  # Last number here is num repetitions, tweak it if times are too small.
        edlib_path SHW $query $target 3    100
    done
done

# HW (infix).
echo_bolded "\nHW, short query (<= 500bp) and long target."
target=$TEST_DATA/E_coli_DH1/e_coli_DH1.fasta
for query_length in 50 100 250 500; do
    echo_underlined "Query length: $query_length"
    for query in $(ls $TEST_DATA/E_coli_DH1/mason_illumina_reads/${query_length}bp/*.fasta); do
        echo "  Query: $query"
        edlib      HW $query $target 3 -1
        edlib_path HW $query $target 3
    done
done

# NW (global).
echo_bolded "\nNW, query and target of equal size, both short (<= 500bp)."
for seq_length in 50 100 250 500; do
    reads_dir=$TEST_DATA/E_coli_DH1/mason_illumina_reads/${seq_length}bp
    target=$reads_dir/e_coli_DH1_illumina_1x${seq_length}.fasta
    echo_underlined "Query and target length: $seq_length"
    echo_underlined "Target: $target"
    for query in $(ls $reads_dir/*.fasta); do
        echo "  Query: $query"
        edlib      HW $query $target 3 -1 100000  # Last number here is num repetitions, tweak it if times are too small.
        edlib_path HW $query $target 3    10000
    done
done

# ----------------------- Long reads ----------------------- #

# HW (infix).
echo_bolded -e "\nHW, long query and long target."
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_underlined "Query: $query"
    edlib      HW $query $target 3 -1
    edlib_path HW $query $target 3
done

# SHW (prefix).
echo_bolded -e "\nSHW, long query and long target."
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_underlined "Query: $query"
    edlib      SHW $query $target 3 -1
    edlib_path SHW $query $target 3
done

# NW (global).
echo_bolded "\nNW, big query and target."
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_underlined "Query: $query"
    edlib      NW $query $target 3 -1
    edlib_path NW $query $target 3
done