使用 GNU Parallel 并行化嵌套 for 循环

Question

我在 Bash 工作。我有一系列嵌套的 for 循环，它们迭代地查找三个包含 96 个条形码序列的列表是否存在。我的目标是找到每个唯一的条形码组合，有 96x96x96 (884,736) 种可能的组合。

for barcode1 in "${ROUND1_BARCODES[@]}";
do
grep -B 1 -A 2 "$barcode1" $FASTQ_R > ROUND1_MATCH.fastq
echo barcode1.is.$barcode1 >> outputLOG

    if [ -s ROUND1_MATCH.fastq ]
    then

        # Now we will look for the presence of ROUND2 barcodes in our reads containing barcodes from the previous step
        for barcode2 in "${ROUND2_BARCODES[@]}";
        do
        grep -B 1 -A 2 "$barcode2" ROUND1_MATCH.fastq > ROUND2_MATCH.fastq

            if [ -s ROUND2_MATCH.fastq ]
            then

                # Now we will look for the presence of ROUND3 barcodes in our reads containing barcodes from the previous step 
                for barcode3 in "${ROUND3_BARCODES[@]}";
                do
                grep -B 1 -A 2 "$barcode3" ./ROUND2_MATCH.fastq | sed '/^--/d' > ROUND3_MATCH.fastq

                # If matches are found we will write them to an output .fastq file itteratively labelled with an ID number
                if [ -s ROUND3_MATCH.fastq ]
                then
                mv ROUND3_MATCH.fastq results/result.$count.2.fastq
                fi

                count=`expr $count + 1` 
                done
            fi
        done
    fi
done

此代码有效，我能够成功提取每个条形码组合的序列。但是，我认为通过并行化这个循环结构可以提高处理大文件的速度。我知道我可以使用 GNU parallel 来执行此操作，但是我正在努力嵌套并行化。

# Parallelize nested loops
now=$(date +"%T")
echo "Beginning STEP1.2: PARALLEL Demultiplex using barcodes. Current 
time : $now" >> outputLOG

mkdir ROUND1_PARALLEL_HITS
parallel -j 6 'grep -B 1 -A 2 -h {} SRR6750041_2_smalltest.fastq > ROUND1_PARALLEL_HITS/{#}_ROUND1_MATCH.fastq' ::: "${ROUND1_BARCODES[@]}"

mkdir ROUND2_PARALLEL_HITS
parallel -j 6 'grep -B 1 -A 2 -h {} ROUND1_PARALLEL_HITS/*.fastq > ROUND2_PARALLEL_HITS/{#}_{/.}.fastq' ::: "${ROUND2_BARCODES[@]}"

mkdir ROUND3_PARALLEL_HITS
parallel -j 6 'grep -B 1 -A 2 -h {} ROUND2_PARALLEL_HITS/*.fastq > ROUND3_PARALLEL_HITS/{#}_{/.}.fastq' ::: "${ROUND3_BARCODES[@]}"

mkdir parallel_results
parallel -j 6 'mv {} parallel_results/result_{#}.fastq' ::: ROUND3_PARALLEL_HITS/*.fastq

如何使用并行成功地重新创建 for 循环的嵌套结构？

Answer 1

仅并行化内循环：

for barcode1 in "${ROUND1_BARCODES[@]}";
do
grep -B 1 -A 2 "$barcode1" $FASTQ_R > ROUND1_MATCH.fastq
echo barcode1.is.$barcode1 >> outputLOG

    if [ -s ROUND1_MATCH.fastq ]
    then

        # Now we will look for the presence of ROUND2 barcodes in our reads containing barcodes from the previous step
        for barcode2 in "${ROUND2_BARCODES[@]}";
        do
        grep -B 1 -A 2 "$barcode2" ROUND1_MATCH.fastq > ROUND2_MATCH.fastq
            if [ -s ROUND2_MATCH.fastq ]
            then
                # Now we will look for the presence of ROUND3 barcodes in our reads containing barcodes from the previous step 
                doit() {
                    grep -B 1 -A 2 "" ./ROUND2_MATCH.fastq | sed '/^--/d'
                }
                export -f doit
                parallel -j0 doit {} '>' results/$barcode1-$barcode2-{} ::: "${ROUND3_BARCODES[@]}"
                # TODO remove files with 0 length
            fi
        done
    fi
done

使用 GNU Parallel 并行化嵌套 for 循环

parallelizing nested for loop with GNU Parallel

bash

loops

pipe

gnu-parallel