Korean, Edit

Collection of Useful Linux Functions

Recommended Article : 【Operating System】 Chapter 1. Linux(Linux)

1. Search for the directory

2. Modify the directory

3. Compress files

4. Query process

5. Execute process

6. Bioinformatics

1. Search for the directory

⑴ Current directory : pwd

⑵ Code to find the number of files in a given directory

ls -l /path/to/directory | grep -v '^d' | wc -l

⑶ Code to find the number of .csv files in a given directory

find /path/to/your/directory -type f -name "*.csv" | wc -l

⑷ Code that outputs the absolute addresses of non-.h5 files in a given directory

find /path/to/directory -type f ! -name '*.h5'

⑸ Code to find out the number of folders in a given directory.

ls -l /path/to/directory | grep '^d' | wc -l

⑹ Code to determine the size of a given file

ls -lh input.bam

⑺ Code to find out the size of a given directory

du -sh /path/to/directory

⑻ Code to view the contents of a zip file without extracting it

unzip -l MyFile.zip

⑼ Code that determines the number of files in a compressed file without extracting it

unzip -l MyFile.zip | wc -l

⑽ Code to display the absolute paths of all files within a certain directory

find /path/to/directory -type f

⑾ Find files containing ‘ABC’, ignoring case differences.

grep -ril "ABC" /path/to/directory

# -r is for recursive search.
# -i ignores case (uppercase/lowercase).
# -l lists only filenames.

⑿ Find files and directories containing ‘ABC’, ignoring case differences

find /path/to/directory -type d -iname "*ABC*" -o -type f -iname "*ABC*"

# -type d searches for directories, -type f for files.
# -iname searches case-insensitively.
# *ABC* is the search pattern (enclosed in asterisks for partial matching).

⒀ Find a file with the exact file name PTPRC.pickle’ in the directory

ls /path/to/folder | grep PTPRC.pickle

⒁ Find files with the exact file name ‘ABC’ in the directory

find /path/to/directory -type f -name "ABC"

⒂ Code to find all .loom files within a specific directory.

find /path/to/directory -maxdepth 1 -name "*.loom" -print

⒃ Find duplicate file names within a particular directory

#!/bin/bash

# Define the target directory
target_directory="/path/to/your/directory"

# Find and list duplicate files based on their MD5 hash
find "$target_directory" -type f -exec md5sum {} + | sort | uniq -d -w 32

⒄ Output time and file information in the order in which files were created in a given directory

ls -ltr --time=creation

2. Modify the directory

⑴ Change ‘ABC’ to ‘ABCD’.

# Renaming Directories and Files (Caution Advised):
## Renaming directories
find /path/to/directory -depth -type d -iname "*ABC*" -execdir rename 's/ABC/ABCD/' '{}' \;

## Renaming files
find /path/to/directory -type f -iname "*ABC*" -execdir rename 's/ABC/ABCD/' '{}' \;

# Replacing Content Inside Files
find /path/to/directory -type f -exec grep -il 'ABC' '{}' \; -exec sed -i 's/ABC/ABCD/gi' '{}' \;

⑵ Remove all subdirectories within a specific directory: that is, extract all files from the subdirectories.

#!/bin/bash

# Base directory containing all target directories
base_directory="/path/to/your/directory"

# Iterate over each directory within the base directory
for target_directory in "$base_directory"/*/; do
    # Find all files and move them with a new name to avoid duplicates
    find "$target_directory" -mindepth 2 -type f -print0 | while IFS= read -r -d $'\0' file; do
        # Construct new filename by replacing '/' with '_' and removing the leading path
        new_name=$(echo "$file" | sed -e "s|$target_directory||" -e 's|/|_|g')
        # Move and rename the file
        mv "$file" "$target_directory$new_name"
    done

    # Remove empty directories
    find "$target_directory" -mindepth 1 -type d -empty -delete
done

3. Compress files

⑴ Compress all files in a specific directory, including subfolders, into test.zip.

zip -r test.zip ./*

⑵ Collecting only files ending with .merged.png and compressing them to .tar.gz

find /path/to/directory -type f -name '*.merged.png' -print0 | tar -czvf merged_png_files.tar.gz --null -T -

4. Query process

⑴ Query for all processes using app.py

ps -ef | grep app.py

5. Execute process

⑴ Running in the background using nohup

① Step 1. Prepare a .sh file or a .py file

② Step 2. Open the terminal

③ Step 3. After setting up the environment, navigate to the directory containing the .sh or .py file to be executed (for example: app.py)

④ Step 4. Grant permission: chmod 755 app.py

⑤ Step 5. Execute with nohup: nohup python app.py \

⑥ Step 6. Press Enter once more to execute

⑦ Step 7. (Optional) To check execution: ps -ef | grep app.py → Check nohup.out. The keyword “app.py” should be recognized

⑧ Step 8. (Optional) To forcibly terminate background execution: kill {ProcessID}

⑵ Loops

6. Bioinformatics

⑴ wc -l filename

① Count the number of lines in the file.

⑵ grep -v ^# gencode.v19.long_noncoding_RNAs.gtf | wc -l

① Output the number of lines in the file excluding those starting with #.

② Role of ^ (caret): ^ represents the start of a line in regular expressions. ^# means “lines starting with #.”

③ Role of -v: -v means the opposite. Without -v, only the lines starting with # would be output.

④ Role of | (vertical bar): Passes the output of the previous command as input to the next command (wc -l).

⑶ grep -w gene gencode.v19.long_noncoding_RNAs.gtf | wc -l

① Output the number of lines in the file that contain the independent word gene.

② Without -w, using grep gene would match any line containing gene, even as part of another word, such as genetics or progene.

Input : 2023.12.28 14:59