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    Using Linux

    Useful Linux Commands

    cd

    Allows you to change the current working directory. 

    $ cd /path/to/directory

    . & ..

    . is the current directory. .. is the parent directory. For example, if you are in the directory /home/user/Documents/my-project, then . is /home/user/Desktop/my-project and .. is /home/user/Documents. So to move backwards in the directory tree, you can use cd ...

    ~

    ~ is the home directory (/home/user by default).

    *

    Wildcard matches all files.

    ls

    Lists the contents of the current directory. 

    $ ls

    Running ls with -s flag will list files or directories with their sizes (in kilobytes). 

    $ ls -s

    cat

    Concatenate reads the contents of a file and prints it to the terminal. 

    $ cat [file]

    column

    Column is super helpful when dealing with csv or any table formated files. 

    $ column -t [file]

    The -s defines the column delimiter.

    When dealing with CSV files, make sure to provide the -n flag too which prevents adjacent delimiters being merged. 

    $ column -t -n -s ',' [file]

    For example, you could have a genotype_report.txt file that looks likes this:

    ID CallRate #AA #AB #BB #NC %AA %AB %BB %NC
27813162 0.185837 141 192 142 2081 0.06 0.08 0.06 0.81
30282025 0.185837 115 240 120 2081 0.04 0.09 0.05 0.81
21928702 0.996870 596 951 1001 8 0.23 0.37 0.39 0.00
27942765 0.241393 142 292 183 1939 0.06 0.11 0.07 0.76

    Which is a little hard to track columns. Using: 

    $ column -t genotype_report.txt

    We get:

    ID        CallRate  #AA  #AB  #BB   #NC   %AA   %AB   %BB   %NC
27813162  0.185837  141  192  142   2081  0.06  0.08  0.06  0.81
30282025  0.185837  115  240  120   2081  0.04  0.09  0.05  0.81
21928702  0.996870  596  951  1001  8     0.23  0.37  0.39  0.00
27942765  0.241393  142  292  183   1939  0.06  0.11  0.07  0.76

    find

    Finds files and directories. 

    $ find [directory to search from] [expression what to find] [what to find]

    $ find Documents -name "*.md"

    Above command will find all files with the extension .md in the Documents directory.

    grep

    Finds all occurences of text in a file. 

    $ grep [string/pattern] [files]

    This will search for and return any lines of text that contain the pattern in given files.

    Helpful flags:

    • -i: Case insensitive search.
    • -c: Count the number of matches.
    • -n: Print the line number of each match.

    |

    Pipe allows you to run multiple commands in a single command. It pipes the standard output of one command into the standard input of the next command. 

    $ cat pedigree.txt | column -t

    The above example would print the file out and pipe the contents into column, which would then format the file.

    Prints the first n lines of a file/input. 

    $ head [file]

    Can specifiy number of lines using -n flag.

    man

    Lookup manual for a given command. 

    $ man [command]

    mkdir

    Creates a new directory. 

    $ mkdir [my-directory]

    mv

    Used to move files and directories. Can also rename files and directories. 

    # move files/directories to new destionation

    $ mv [files/directories] [destination]

    # rename file/directory

    $ mv [file/directory] [new name]

    cp

    Copy files and directories. 

    $ cp [files/directories] [destination]

    pwd

    Print working directory will output the path of the current working directory. 

    $ pwd

    sudo

    Sudo is used to temporaily gain/give administrative privileges. If any command is restricted, use sudo before the given command. It will then prompt for your password. 

    $ sudo [command]

    rm

    Remove command removes files and directories. 

    # simple file remove

    $ rm [path/to/file]

    # remove directory

    $ rm -r [path/to/directory]

    # remove multiple files

    $ rm [path/to/file1] [path/to/file2]

    wc

    Count the number of lines, words, characters, and bytes in a file or input. 

    $ wc [options] [file]

    For example: 

    $wc pedigree.txt

    Will look something like this:

    397 4222 22566 /pedigree.txt
    • 397 is the number of lines.
    • 4222 is the number of words.
    • 22566 is the number of characters.

    You can also pass in multiple files.

    Important flags:

    • -l, –lines - Print the number of lines.
    • -w, –words - Print the number of words.
    • -m, –chars - Print the number of characters.
    • -c, –bytes - Print the number of bytes.

    awk

    Awk is a language that can be used to manipulate text files. It is useful for transforming data files and producing formatted reports.

    The syntax is: 

    $awk options 'selection criteria' [input-file] > [output-file]

    For example, lets say you have this pedigree file:

    9997515 5017534 7651593
9939593 5765357 6245551
9998766 5455357 7736346
9954672 5017534 6245551
9999762 5455357 6245551

    To print out the file: 

    $ awk '{print}' pedigree.txt

    If you wanted to see every line with a certain id, you could do this: 

    $ awk '{if ($1 == "9997515") print}' pedigree.txt

    Outputs:

    9997515 5017534 7651593

    Imagine you wanted to find the id of an animal that had two certain parents. You could do this: 

    $ awk '{if($2 == "5017534" && $3 == "7651593") {print}}' pedigree.txt

    Outputs:

    9997515 5017534 7651593

    If you only want to print certain columns, you can use the $0, $1, $2 …. $0 means to print every column, then $1, $n, denotes each column from 1 to n. For example: 

    $ awk '{print $1}' pedigree.txt

    Outputs:

    9997515
9939593
9998766
9954672
9999762