04_bash_examples.txt

# 4. More Shell Concepts 


# Parameter expansion

v="hello"

# Notice the difference between single and double quotes. One allows
# shell variable expansion, the other does not.
echo "${v} there"
echo '${v} there'
# Backslash can be used to "escape" a special character to stop the
# shell from interpreting it as special
echo "\${v} there"
# Print the length of a variable
echo ${#v}
# Extract a substring
echo ${v:0:3}
# Substrings are interpreted as "maths", so can calculate values
echo ${v:2:${#v}-3}

# A more useful example
v="temp_salt_jun.grb.txt"

# Remove .txt suffix
echo ${v%.txt}

# As above, but with using substitution with an empty string
echo ${v/.txt/}

# More useful substitution when converting from grib to netcdf
echo ${v/.grb.txt/.nc}

# Command substitution
ls -l $(which ls)


# Subshells

# Make some temporary directories
mkdir {00..10}
# Descend into each directory in a subshell, and make a file
for d in {00..10}; do (cd $d && touch tempfile) done
ls -l ??
# Remove all the files in the directories and then remove the
# directories
rm {00..10}/*
rmdir {00..10}
# Could have used rm -r {00..10} but BE CAREFUL WITH RECURSIVE FLAG
# Good idea to use ls to list the file match/glob you want to do an
# operation on, then use history to pull back that command and change
# ls to the dangerous operation


# Aliases

# make an alias
alias ls="ls --color"
# list aliases
alias

# Put them in your .bashrc file to make them permanent
echo "alias ls='ls --color'" >> ~/.bashrc

# Similar to shell builtins above, the which command will give 
# misleading information about aliases:
which ls
type ls


# Output redirection

# Only capture standard out
set +e
ls MM* *.* > log
# Put standard error and standard out into the same file ...
ls MM* *.* &> log
# ... separate files
ls MM* *.* 1> log.out 2> log.err 
set -e

# Running shell scripts

# Make a silly shell program
echo "echo Running myprog" > myprog

# If you try to run this program you will get a permission
# denied error. 
set +e
myprog
set -e

# You can instead explicitly tell bash to create a new shell to
# run the script
bash myprog

# .. or use the current shell (. is the same as bash command source)
source myprog
. myprog

# In the first example the shell found the file but it does not 
# have execute permission. Change the permissions and try again
chmod a+x myprog
myprog 
./myprog

# Often a shell (or python, perl) program will have a "shebang" or 
# "hashbang" in the first line. This tells the shell what program 
# to use to run it
rm myprog
echo "#!"$(which python) > myprog
echo "print(\"This is python\")" >> myprog
chmod a+x myprog
./myprog
cat myprog


# More looping

# Three ways to accomplish the same thing, loop through from 1 to 10
for i in $(seq 1 10); do echo -n $i; done
for ((i=1;i<=10;i++)); do echo $i; done
for i in {1..10}; do echo $i; done

# The last method has a nice side effect of zero padding numbers
# automatically, which can be nice when creating filenames that
# list nicely automatically
for i in {001..10}; do echo $i; done

# Compare ...
for i in {1..10}; do touch tmp/file_$i.txt; done
ls -l tmp
rm tmp/*
# .. and contrast
for i in {001..10}; do touch tmp/file_$i.txt; done
ls -l tmp

# The bash variable substitution is now very powerful when combined
# with loops. 

# Systematically change the name of files (echo first to check what
# the command will do, then run the command without echo
for file in tmp/file_???.txt; do echo mv $file ${file/file/output}; done
for file in tmp/file_???.txt; do mv $file ${file/file/output}; done

# Systematically change file extension. Especially useful when using a 
# program to transform a file from one format to another, e.g. using 
# convert from ImageMagick to change from one image format to another

# Use wget to download a picture of a phytoplankton bloom in Shark Bay.
# Note the -O option is used to specify the name of the downloaded file
wget https://goo.gl/11DSGh -O Shark_Bay.jpg

# Make 10 copies of the Shark Bay image file
for i in {1..10}; do cp Shark_Bay.jpg tmp/shark_bay_$i.jpg; done

# Loop through the copies and convert each to a TIFF file, using 
# pattern substitution to match a '.jpg' extension and replace with 
# '.tiff'
for file in tmp/shark_bay_*; do convert $file ${file/%.jpg/.tiff}; done

# Conditional execution

# As mentioned in the software carpentry material, two commands
# can be put on the same line, separated by a semicolon and one
# command will execute after the other but there is no check the
# first command completed successfully
sleep 5; ls

# Execute subsequent commands based on success or failure of 
# previous commands. 

# && stands for "and" which means if the previous command 
# returns an error code the subsequent commands will not run
sleep 5 && ls
# || stands for "or" and has the opposite meaning to &&
sleep 5 || ls

# Important if there is a dependency on the first command 
# running before subsequent commands
set +e
mkdir /lala ; ls /lala
mkdir /lala && ls /lala
set -e