Introduction_to_linux

Why Unix

Is a stanadrd operating system in most computer systems in scientific research. It can handle large amount of data in different file formats. i.e text files, fasta files

basic command-line

1. pwd command - prints your current working directory (.)

list each of the folders you would need to navigate through to get from the root of the file system to your current directory.

2. cd - changes your directory

3. ls - list the contents of a directory

used to list the contents of a directory. ls command can be given different options i.e -l -a -h

4. mkdir command

used for making a directory has option uasge: mkdir -p outer/inner

The root directory

/home/evans/mudibo

• home is the parent directory for evans to move up to levels from mudibo directory type cd ../.. - absolute path cd .. - relative path . means current working directory .. means parent directory one level up from current working directory

changing directory way back home

1. cd
2. cd /
3. cd ~ 

Man pages

for command lines that have different options e.g ls less sort cd

Removing/Deleting files and directories

for file use rm rm -i gives opportunity to confirm if you are sure you want to delete for directory rm -r any empty directory can be removed by rmdir

tab completion

tab completion is used to complete a command or a directory or a file

touch command

for creating new empty file

mv command

used to move a file or a directory

wildcards * and ?

• matches against none or more characters in a file (or directory) name usage: ls list* - this will list all files in the current directory starting with **list... ls *list - will list all files in the current directory ending with ....list

? character matches exactly one character. i.e ls ?ouse will match files like house and mouse, but not grouse

cp command

for copying files and directories cp -r for copying a directory

clear command

clears the terminal with of the previous commands.

cat (concatenate) command

displays the contents of a file on the screen also used to combine files

less command

writes the contents of a file onto the screen a page at a time. press the space-bar for next page type q to quit less command can also be used for searching a given content in the file type less /

grep command

searches files for specified words or patterns. it is case sensitive. to ignore case distinctions, -i option is used i.e. grep -i science Science science.txt to search for a phrase or pattern, single quotes are used grep -i 'biology of human diseases' science.txt other grep options -v displays those lines that dont match -n precede each matching line with the line number -c print only the toal count of matched lines

wc command

used for word count wc -w counts words wc -l counts lines wc -m counts characters

mv command can also be used in renaming files

mv file1 file2 - renames file1 to be file2

nano command

for editing a file

echo

displays information of environment variables they contain user-specific or system-wide values that either reflect simple pieces of information (your username), or lists of useful locations on the file system echo is also used to append the data to an existing file.

wget command

downloading file using the location link of a given file

curl command

download the contents of any URL you provide it and print it to STDOUT to download the content in the filesystem you redirect the output of curl to the file i.e. curl https://classroom.google.com/u/1/c/Mzc4Mjc5MjA5MDZa/a/NDE5NDkxMjI4NjVa/details > outputfile

pipe | command

connects two unix programs

View  10 lines of a file (using head and tail commands):

tail -n 20 file.txt | head

Show lines of a file that begin with a start codon (ATG) (the ^ matches patterns at the start of a line):

grep "^ATG" file.txt

Cut out the 3rd column of a tab-delimited text file and sort it to only show unique lines (i.e. remove duplicates):

cut -f 3 file.txt | sort -u

Count how many lines in a file contain the words 'cat' or 'bat' (-c option of grep counts lines):

grep -c '[bc]at' file.txt

Turn lower-case text into upper-case (using tr command to 'transliterate'):

tr 'a-z' 'A-Z' < file.txt

Change all occurences of 'Chr1' to 'Chromosome 1' and write changed output to a new file (using sed command):

sed 's/Chr1/Chromosome 1/g' file.txt > file2.txt

gzip

compresses a file i.e. gzip science.txt

pipes

connects the output of command to be input of of another command. the symbol for pipe is the vertical bar |

Changing the access rights (chmod)

only the ownwer of a file can use chmod to change the permissions of a file. options include u user g group o other a all r read w write(and delete) x execute(and acess directory)

• add permission i.e.

to remove read write and execute permissions on a science.txt file for the group and others, type % chmod go-rwx science to give read and write permissions on the science.txt file to all, type chmod a+rw science.txt