How to move multiple files to multiple folders in linux?

Question

I have a folder containing *.fastq.gz files (R1 and R2) for many samples. For example, in the folder "Raw_WGS", I have several files like

Sample_1_R1.fastq.gz, Sample_1_R2.fastq.gz, Sample_2_R1.fastq.gz, Sample_2_R2.fastq.gz, Sample_3_R1.fastq.gz, Sample_3_R2.fastq.gz

I have another folder e.g. "Analysis" where I have different sub-folders according to the name of my sample sequences. I have sub-folders named like

Sample_1, Sample_2, Sample_3

I have a Text file containing all and ONLY the names of my samples i.e. Sample_1, Sample_2, Sample_3. Now, I want to move the *_R1.fastq.gz and *_R2.fastq.gz files for each sample to their respective sub-folder according to the name in the "Analysis" folder.

Can you please tell me how can I do that for all the samples at once? I can use the mv command to move each file at a time. But I have 1000s of files. So, I want to move them all by running a single script. Please let me know if you have any suggestions.

• Chris Davies: Loop across the directory names, and move matching files
• Andre Wildberg: This might help unix.stackexchange.com/questions/527073/…

Answer 1

If I understand you correctly, you don't need a file with the names, since they are already in the file names. Try this:

for i in *_R{1,2}.fastq.gz; do 
 # use `cp` to be sure it works
 cp "$i" /path/toAnalisys/"${i%_*}"
done

Answer 2

Assuming Samples.txt contains Sample_1 till 3 one per lne , we can setup an xargs command to call mv

tree -F
< Samples.txt \
xargs -I {} -t mv -t Analysis/{}/ \
 Raw_WGS/{}_R1.fastq.gz \
 Raw_WGS/{}_R2.fastq.gz ;
tree -F

Results:

Before move...
 .
├── Analysis/
│  ├── Sample_1/
│  ├── Sample_2/
│  ├── Sample_3/
│  ├── Sample_4/
│  └── Sample_5/
└── Raw_WGS/
 ├── Sample_1_R1.fastq.gz
 ├── Sample_1_R2.fastq.gz
 ├── Sample_2_R1.fastq.gz
 ├── Sample_2_R2.fastq.gz
 ├── Sample_3_R1.fastq.gz
 └── Sample_3_R2.fastq.gz
After move...
.
├── Analysis/
│  ├── Sample_1/
│  │  ├── Sample_1_R1.fastq.gz
│  │  └── Sample_1_R2.fastq.gz
│  ├── Sample_2/
│  │  ├── Sample_2_R1.fastq.gz
│  │  └── Sample_2_R2.fastq.gz
│  ├── Sample_3/
│  │  ├── Sample_3_R1.fastq.gz
│  │  └── Sample_3_R2.fastq.gz
│  ├── Sample_4/
│  └── Sample_5/
└── Raw_WGS/