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#!/bin/bash
#store benchmark time and memory
tempfile=time_mem.tmp
#record memory
memorys=()
#record elapsed time
times=()
#number of programs
num=-1
#number of repeat tests
repeats=$1
#input fasta files
gfiles=$@
measure_memory_time(){
/usr/bin/time -f "%e %M" -o $tempfile $1 > /dev/null 2>&1
let num++
if [ ! ${memorys[$num]} > 0 ]; then
memorys[$num]=0
times[$num]=0
fi
arr=($(cat $tempfile))
#clear temp file
if [ -e "$tempfile" ]; then
rm "$tempfile"
fi
times[$num]=$(echo "${arr[0]}+${times[$num]}" | bc)
memorys[$num]=$(echo "${arr[1]}+${memorys[$num]}" | bc)
}
#print header
printf "genome\tsize\tcount\tbioperl\t\tbiopython\t\tpyfaidx\t\tpyfasta\t\tpysam\t\tpyfastx1\t\tpyfastx2\t\tpyfastx3\t\tpyfastx4\t\n"
for gfile in ${gfiles[@]:1}; do
memorys=()
times=()
filename=$(basename $gfile)
filename="${filename%.*}"
#get longest sequence name
array=($(python3 get_fasta_info.py $gfile))
#genome size
gsize=${array[0]}
#sequence counts in genome
seqcounts=${array[1]}
for i in $(seq 1 $repeats); do
num=-1
#bioperl
measure_memory_time "perl bioperl_fasta_sequence_iterate.pl $gfile"
#biopython
measure_memory_time "python3 biopython_fasta_sequence_iterate.py $gfile"
#pyfaidx
measure_memory_time "python3 pyfaidx_fasta_sequence_iterate.py $gfile"
#pyfasta
measure_memory_time "python3 pyfasta_fasta_sequence_iterate.py $gfile"
#pysam1 with index
#measure_memory_time "python3 pysam_fasta_sequence_iterate_with_index.py $gfile"
#pysam2 without index
measure_memory_time "python3 pysam_fasta_sequence_iterate.py $gfile"
#pyfastx1 with index
measure_memory_time "python3 pyfastx_fasta_sequence_iterate_with_index.py $gfile"
#pyfastx2 without index
measure_memory_time "python3 pyfastx_fasta_sequence_iterate_without_index.py $gfile"
#pyfastx3 with gzip index
measure_memory_time "python3 pyfastx_fasta_sequence_iterate_with_index.py $gfile.gz"
#pyfastx4 without gzip index
measure_memory_time "python3 pyfastx_fasta_sequence_iterate_without_index.py $gfile.gz"
done
#print result
printf "%s\t%s\t%s" $filename $gsize $seqcounts
for((i=0;i<=$num;i++)); do
mm=$(echo "${memorys[$i]}/$repeats" | bc)
et=$(echo "${times[$i]}/$repeats" | bc)
printf "\t%d\t%d" $mm $et
done
printf "\n"
done
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