linux basics

ngs2014_linux_basics.sh

#linux commands basics
#http://software-carpentry.org/v5/novice/shell/index.html
# practise, practise, practise, google, google, google and you will get it :)

pwd  # print working directory
cd   # change directory
sudo  # super user privilege
chmod 775 # change the privileges  http://en.wikipedia.org/wiki/Chmod
git clone # version control! get to know git and github! http://git-scm.com/ 
sudo bash  # bad habit
whoami    # who you are
exit 
logout 
echo  # it's like print 
ls -sh # give the size information in MB etc 
ls -F  # color your folders vs files
ls -l  # long format
ls -a  # list everything including invisible files
ls /home/tommy/data  # list files in the data folder by specifying a full path

clear # clear the screen 

# remember the tab magic auto-fill
# clarify the filesystem: slash  / denotes the root directory   ~ denotes the home directory

cd -  # change directory to your previous directory
cd ~ or just cd   # change directory to your home directory
cd ..   # change directory one level up
cd ../.. # change directory to two levels up

cp  /home/tommy/data.txt .   # copy data.txt to the current directory which denoted by .

# create things txt editors!

nano   # use this one, because it is easy
emacs  # do not use it until later stage
vi     # 90% of the people do not know how to exit vim :)

cat mydata.txt # print the content of mydata.txt to the stand output(the screen)
cat mydata1.txt mydata2.txt > total_data.txt   # concatenate two files to a new file

ctrl + D  # quit (indicate cat that this is the last line) when you do something like: cat > mydata.txt

head -15 # print the first 15 lines to the screen 
tail     # print the last 10 lines to the screen by default
less     # use less to peek txt files. less is more

#get help
man  # man cat  will show you all the flags (arguments) for cat command
info


# control + c to quit any command 

rm  # dangerous remove files (permanetly gone) 

rm -fr  #remove directory 

move # rename files

move mydata.txt my_new_data.txt  # rename mydata.txt to my_new_data.txt


cp # copy files. do not put space in your file names in linux, just remember it.

#############################

# text manipulation  again use man to explore the flags for all the commands below or google it!
sed  #  a book can be dedicated to explain the usage of it http://www.thegeekstuff.com/sed-awk-101-hacks-ebook/
awk  # a book can be dedicated to explain the usage of it http://www.thegeekstuff.com/sed-awk-101-hacks-ebook/

cut  # one of the most frequently commands I use, cut the columns out of a txt file
cut -f1,3 mydata.txt # cut out the first and third columns out and print it to screen

paste # paste two files side by side

comm  # look common lines of two files, files need to be sorted first.

comm -12   # will supress the unique lines in each file

diff  # look different lines of two files.

wc  # word count
wc -l # line number

grep ATCG mydata.txt | head  # find lines containing ATCG in mydata.txt and look at it by head
grep -v ATCG mydata.txt > no_ATCG.txt # find lines not containing ATCG and redirect to a new file named no_ATCG.txt

nl    # number lines of your output

sort -k2,2 -nr    # reverse numerical sort based on my second column 

###############################

#up-arrow to reuse your previous command
control + r  #reverse search your command
history      # your command history

# redirect with >, instead print the output in the command screen, redirect it to a new file

head -n 1000 mydata.txt > newdata.txt   
# redirect the first 1000 lines to a new file named newdata.txt

ls . > file_names.txt
# redirect all the file names in the current directory to a file named file_names.txt


##########################

# pipes  |  where the power comes

history | less   # look at your history by less, type q to quit less

cat mydata.txt | sort -k2,2 -nr > whole_sorted_data.txt  # I am a useless cat fan

# the upper one equals to 
sort -k2,2 -nr mydata.txt> whole_sorted_data.txt

head -n 1000 mydata.txt | sort -k2,2 -nr > my_selected_sorted_data.txt

###########################

# use wildcard  characters * ? .
# again regular expressions! http://regexone.com/

##################### loops

for file in *.xml; do head -3 $file; done

for file in *.xml; do head -3 $file >> all_head3_xml.txt; done

for file in *.xml; do head -3 ${file} > ${file}.txt; done  # rename the files by adding txt suffix keeping the old name of the *.xml files.