连接子目录下的多个文件

Question

我的目录结构如下

x:\Project_2012-158A\Sample_4041

SampleSheet.csv
4041_CGTACG_L002_R1_001.fastq
4041_CGTACG_L002_R2_001.fastq
4041_CGTACG_L006_R2_001.fastq
4041_CGTACG_L006_R1_001.fastq

x:\Project_2012-158A\Sample_4027

SampleSheet.csv
4027_TAGCTT_L002_R2_001.fastq
4027_TAGCTT_L006_R1_001.fastq
4027_TAGCTT_L002_R1_001.fastq
4027_TAGCTT_L006_R2_001.fastq

x:\Project_2012-158A\Sample_D425

SampleSheet.csv
D425_ACTGAT_L008_R2_001.fastq
D425_ACTGAT_L008_R1_001.fastq
D425_ACTGAT_L004_R2_001.fastq
D425_ACTGAT_L004_R1_001.fastq

我想为每个样本分别将文件与“R1”和“R2”连接起来。我知道

cat file1.fastq file2.fastq > concatenation.fastq 

将提供 concatenate 但我如何使用单个脚本为所有 sudirectories 执行此操作？

Answer 1

cd /path/to/Project_2012-158A &&
for dir in Sample*/; do
    for r in R1 R2; do
        outfile=${dir%/}_${r}.fastq
        glob=*_${r}_*.fastq
        cat "$dir"/$glob > "$dir/$outfile" &&
        rm -f "$dir"/$glob
    done
done