9 min to read

Managing Files and Directories in Unix

Essential Commands for Copying, Moving, and Organizing Your Bioinformatics Data

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In this lesson we will learn how to copy the files, move them around, and rename them. We we will also learn how to use standard output to write to files.

Why File Management Matters

In bioinformatics, you’ll work with hundreds or thousands of files—raw data, analysis results, scripts, and references. Knowing how to efficiently copy, move, and organize files is essential for:

Let’s explore the core commands that make this possible.

Copying Files: The cp Command

Basic File Copying

The cp (copy) command creates a duplicate of a file. The basic syntax is:

cp <original_filename> <new_filename>

Example: Copying in the same directory

cp tiny_n_L001_R1_xxx.fastq.gz tiny_n_L001_R1_xxx.fastq.gz.copy 
ls

This creates a duplicate with a new name. Both files now exist independently—changes to one won’t affect the other.

Copying to Different Directories

You can copy files to other locations while keeping or changing the filename:

# Create a new directory for copies
mkdir fastq_copies

# Copy with a new filename
cp yeast_01_R2.fastq.gz fastq_copies/yeast_01_R2.fastq.gz.copy


# Copy with the same filename
cp yeast_02_R2.fastq.gz fastq_copies/

# Verify the copies
ls fastq_copies/

You have noticed that even if you do not mention the name of the orignal name of the file is used and is placed in the new directory.

What happened here?

When to Use cp

Moving and Renaming: The mv Command

The Dual Purpose of mv

Unlike cp, the mv (move) command doesn’t create a copy—it relocates or renames the file. The original disappears from its previous location.

Syntax:

mv <original_filename> <new_filename_or_location>

Moving Files Between Directories

mv tiny_n_L001_R1_xxx.fastq.gz.copy fastq_copies/
cd fastq_copies
ls

The file is now only in fastq_copies/—it no longer exists in the original directory.

Renaming Files

mv yeast_01_R2.fastq.gz copy-yeast_01_R2.fastq.gz
ls

When both arguments are in the same directory, mv renames the file instead of moving it.

When to Use mv

⚠️ Caution: mv is destructive—the original location/name is gone. Double-check your commands!

Removing Files: The rm Command

Deleting Individual Files

The rm (remove) command permanently deletes files. There is no recycle bin or undo!

Warning: There is no recycle bin or undo!

You can try the following command to delete the following file.

rm tiny_n_L001_R1_xxx.fastq.gz.copy

💡 Safety tip: Always double-check filenames before pressing Enter. Consider using ls first to verify the file exists.

Removing Directories

To delete a directory and all its contents, use the -r (recursive) flag:

cd ..
rm -r fastq_copies/

The -r flag tells rm to:

  1. Enter the directory
  2. Delete all files inside
  3. Delete all subdirectories and their contents
  4. Delete the directory itself

Removing Empty Directories

For empty directories, you have two options:

rm -r empty_directory/
# OR
rmdir empty_directory/

The rmdir command only works on empty directories—it’s a safer option when you want to ensure nothing important gets deleted.

Critical Safety Warning

🚨 The rm command is permanent!

Best practices:

Understanding Standard Output

The echo Command

echo prints text to the screen (standard output or “stdout”):

echo 'Hello, World.'

Output:

Hello, World.

Quotes: When Are They Needed?

Let’s experiment:

echo 'hello'
echo hello

Both produce:

hello

So far, quotes seem optional. But watch what happens with special characters:

echo hello!!

Output:

echo helloecho hello!
helloecho hello!

What went wrong? The !! has special meaning in bash (history expansion). Now with quotes:

echo 'hello!!'

Output:

hello!!

When to use quotes:

Output Redirection: Writing Files

The > Operator (Overwrite)

Instead of printing to the screen, we can redirect output to a file using >:

echo hello > hello.txt

This creates hello.txt with the content “hello”. If hello.txt already exists, it will be overwritten!

echo hello > hello.txt
echo hello > hello.txt  # Still just one "hello"
cat hello.txt

Output:

hello

Each > overwrites the previous content.

The >> Operator (Append)

To add content to the end of a file without overwriting, use >>:

echo hello >> hellohello.txt
echo hello >> hellohello.txt
cat hellohello.txt

Output:

hello
hello

Each >> adds a new line to the file.

Practical Applications

Creating sample files:

echo ">sequence1" > sample.fasta
echo "ATCGATCGATCG" >> sample.fasta
echo ">sequence2" >> sample.fasta
echo "GCTAGCTAGCTA" >> sample.fasta

Logging analysis results:

echo "Analysis started: $(date)" > analysis_log.txt
echo "Processing sample1..." >> analysis_log.txt
echo "Completed successfully" >> analysis_log.txt

Creating metadata files:

echo "sample_id\tcondition\treplicate" > metadata.tsv
echo "sample1\tcontrol\t1" >> metadata.tsv
echo "sample2\ttreated\t1" >> metadata.tsv

Quick Reference Table

Command Purpose Example Caution
cp Copy files cp data.txt backup.txt Creates duplicate
mv Move/rename mv old.txt new.txt Original removed
rm Delete files rm temp.txt Permanent!
rm -r Delete directories rm -r temp_folder/ Very dangerous!
> Write/overwrite echo "text" > file.txt Overwrites existing
>> Append echo "text" >> file.txt Adds to end

Practice Exercise

Try these commands to reinforce your learning:

  1. Create a directory called practice
  2. Copy a FASTQ file into it with a new name
  3. Create a text file using echo > with your name
  4. Append your favorite organism to that file using >>
  5. Rename the text file using mv
  6. Move the FASTQ file back to the parent directory
  7. Remove the practice directory

Solution:

mkdir practice
cp yeast_01_R1.fastq.gz practice/practice_file.fastq.gz
echo "Your Name" > practice/info.txt
echo "Favorite organism: Yeast" >> practice/info.txt
cd practice
mv info.txt myinfo.txt
mv practice_file.fastq.gz ../
cd ..
rm -r practice/

Common Mistakes to Avoid

❌ Using rm -r without double-checking

rm -r important_data/  # Oops, meant to delete temp_data/

❌ Overwriting important files with >

echo "test" > critical_results.txt  # Just erased everything!

❌ Forgetting -r when removing directories

rm data_folder/  # Error: cannot remove directory

✅ Safe practices:

ls data_folder/      # Check contents first
rm -r data_folder/   # Then remove

What’s Next?

In Lesson 07, we’ll explore:

Key Takeaways

✓ cp creates copies, keeping the original intact
✓ mv moves or renames files—the original location/name disappears
✓ rm permanently deletes files with no recovery option
✓ Use -r flag to remove directories and their contents
✓ > overwrites files, >> appends to files
✓ Always double-check commands before deleting files
✓ Use quotes with echo to avoid issues with special characters.

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