我正在使用Bash进行工作。我有一系列嵌套的for循环,迭代地查找三个96个条形码序列列表的存在。我的目标是找到每个独特的条形码组合,共有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 $count + 1`
done
fi
done
fi
done
这段代码可以正常运行,我能够成功地提取每个条形码组合的序列。然而,我认为通过并行化循环结构,可以提高处理大文件的速度。我知道可以使用GNU parallel来实现这一点,但是我在嵌套并行化方面遇到了困难。
# Parallelize nested loops
now=$(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
如何使用并行方式成功地重新创建for循环的嵌套结构?
xargs -P 0
命令,它会自动创建所需数量的线程。我正在使用xargs
将多个 mp4 文件转换为 mp3,性能有了很大提升。parallel
的功能相同,但语法稍微复杂一些。 - Shakiba Moshiri