使用reformat.sh（bbmap）进行批量操作

Question

我有一个文件夹，其中包含以下格式的双端测序数据：

Bk1-ITS2_S102_L001_R1_001.fastq.gz
Bk1-ITS2_S102_L001_R2_001.fastq.gz
Bk2-ITS2_S103_L001_R1_001.fastq.gz
Bk2-ITS2_S103_L001_R2_001.fastq.gz
Fl1-ITS2_S201_L001_R1_001.fastq.gz
Fl1-ITS2_S201_L001_R2_001.fastq.gz
Fl2-ITS2_S202_L001_R1_001.fastq.gz
Fl2-ITS2_S202_L001_R2_001.fastq.gz
Mn1-ITS2_S401_L001_R1_001.fastq.gz
Mn1-ITS2_S401_L001_R2_001.fastq.gz
Mn2-ITS2_S402_L001_R1_001.fastq.gz
Mn2-ITS2_S402_L001_R2_001.fastq.gz

我想使用循环或一些通配符对整个文件夹运行以下命令，因为对每对读取执行此操作很麻烦并且需要很多时间：

reformat.sh in=Bk1-ITS2_S102_L001_R1_001.fastq.gz in2=Bk1-ITS2_S102_L001_R2_001.fastq.gz   out=./reformat/Bk1-ITS2_S102_L001_R1_001_reformatted.fastq.gz out2=./reformat/Bk1-ITS2_S102_L001_R2_001_reformatted.fastq.gz mincalledquality=2 maxcalledquality=41 qin=33

这样我就可以为所有具有修改后的质量分数的文件实现以下目标，并在每个文件的名称中添加一个“重新格式化”的附加字符串。

Bk1-ITS2_S102_L001_R1_001_reformatted.fastq.gz
Bk1-ITS2_S102_L001_R2_001_reformatted.fastq.gz
Bk2-ITS2_S103_L001_R1_001_reformatted.fastq.gz
Bk2-ITS2_S103_L001_R2_001_reformatted.fastq.gz
Fl1-ITS2_S201_L001_R1_001_reformatted.fastq.gz
Fl1-ITS2_S201_L001_R2_001_reformatted.fastq.gz
Fl2-ITS2_S202_L001_R1_001_reformatted.fastq.gz
Fl2-ITS2_S202_L001_R2_001_reformatted.fastq.gz
Mn1-ITS2_S401_L001_R1_001_reformatted.fastq.gz
Mn1-ITS2_S401_L001_R2_001_reformatted.fastq.gz`
Mn2-ITS2_S402_L001_R1_001_reformatted.fastq.gz
Mn2-ITS2_S402_L001_R2_001_reformatted.fastq.gz

我一次只能进行一对读取。 有人可以帮助我如何实现这一目标吗？

Answer 1

这是使用 bash 执行此操作的一种方法（我认为“`”是一个拼写错误）：

for f in *fastq.gz; do mv $f ${f/.*fastq.gz/}_reformatted.fastq.gz; done