Text handling commands
Text handling commands
command > file
saves STDOUT in a file
command >> file
appends STDOUT in a file
cat file
concatenate and print files
cat file1 file2 > file3
merges files 1 and 2 into file3
cat *fasta > all.fasta
concatenates all fasta files in
the current directory
head file
prints first lines from a file
head -n 5 file
prints first five lines from a file
tail file
prints last lines from a file
tail -n 5 file
prints last five lines from a file
less file
view a file
less -N file
includes line numbers
less -S file
wraps long lines
grep āpatternā file
Prints lines matching a pattern
grep -c āpatternā file
counts lines matching a pattern
cut -f 1,3 file
retrieves data from selected
columns in a tab-delimited file
sort file
sorts lines from a file
sort -u file
sorts and return unique lines
uniq -c file
filters adjacent repeated lines
wc file
counts lines, words and bytes
paste file1 file2
concatenates the lines of input
files
paste -d ā,ā
concatenates the lines of input
files by commas
sed
transforms text
File system Commands
File system Commands
ls
lists directories and files
ls -a
lists all files including hidden files
ls -lh
formatted list including more data
ls -t
lists sorted by date
pwd
returns path to working directory
cd dir
changes directory
cd ..
goes to parent directory
cd /
goes to root directory
cd
goes to home directory
touch file_name
creates en empty file
cp file file_copy
copy a file
cp -r
copy files contained in directories
rm file
deletes a file
rm -r dir
deletes a directory and its files
mv file1 file2
moves or renames a file
mkdir dir_name
creates a directory
rmdir dir_name
deletes a directory
locate file_name
searches a file
man command
shows commands manual
top
shows process activity
df -h
shows disk space info
apt-get install
installs applications in linux
Networking Commands
Networking Commands
wget URL
download a file from an URL
ssh user@server
connects to a server
scp
copy files between computers
Compression commands
Compression commands
gzip/zip
compress a file
gunzip/unzip
decompress a file
tar -cvf
groups files
tar -xvf
ungroups files
tar -zcvf
groups and gzip files
tar -zxvf
gunzip and ungroups files
UNIX Command-Line Cheat Sheet
BTI-SGN Bioinformatics Course 2014
