Quick script to compare two versions of sra-human-scrubber

test-scrubber.sh

#! /bin/bash

SCRUBBER_DB=${SCRUBBER_SHARE}/data/human_filter.db

# Current scrubber
echo "Run test on current Scrubber"
which scrub.sh
scrub.sh test

echo "Run test on PR Scrubber"
sra-human-scrubber/scripts/scrub.sh -t -d ${SCRUBBER_SHARE}/data/human_filter.db

echo "Compare scrubbers"
printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" "fastq" "input_size" "current_runtime" "gunzip_runtime" "scrub_runtime" "gzip_runtime" "pr_runtime" "current_md5" "pr_md5" "md5s_equal"
rm -rf current_scrubber pr_scrubber
mkdir current_scrubber pr_scrubber
for f in fastqs/*.fastq.gz; do
    file_size=$(du ${f} -b | cut -f 1)
    file_name="$(basename ${f%%.*})"
    # Test urrent scrubber
    start=`date +%s`
    start_gunzip=`date +%s`
    gunzip -c ${f} > current_scrubber/${file_name}.fastq
    end_gunzip=`date +%s`
    start_scrub=`date +%s`
    scrub.sh current_scrubber/${file_name}.fastq
    end_scrub=`date +%s`
    start_gzip=`date +%s`
    gzip current_scrubber/${file_name}.fastq.clean
    end_gzip=`date +%s`
    rm current_scrubber/${file_name}.fastq
    end=`date +%s`
    current_runtime=$((end-start))
    current_gunzip=$((end_gunzip-start_gunzip))
    current_scrub=$((end_scrub-start_scrub))
    current_gzip=$((end_gzip-start_gzip))
    current_fastq="current_scrubber/${file_name}.fastq.clean.gz"

    # test PR scrubber
    pr_fastq="pr_scrubber/${file_name}.clean.fastq.gz"
    start=`date +%s`
    zcat ${f} | sra-human-scrubber/scripts/scrub.sh -d ${SCRUBBER_SHARE}/data/human_filter.db | gzip > ${pr_fastq}
    end=`date +%s`
    pr_runtime=$((end-start))

    # test md5s of fastq contents
    current_md5=$(zcat ${current_fastq} | md5sum | cut -d " " -f 1)
    pr_md5=$(zcat ${pr_fastq} | md5sum | cut -d " " -f 1)
    md5s_equal="false"
    if [ "${current_md5}" == "${pr_md5}" ]; then
        md5s_equal="true"
    fi

    printf "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" "${f}" "${file_size}" "${current_runtime}" "${current_gunzip}" "${current_scrub}" "${current_gzip}" "${pr_runtime}" "${current_md5}" "${pr_md5}" "${md5s_equal}"
done