Script

Script#

Creating a Script#

First, create a file with the *.sh extension.

Next, open your script and put the following at the top:

#!/bin/bash

Arrays#

Create array from list of files

FILES=($(ls -r data*.*))

Use array (just an example)

${FILES[2]}

Strings#

Get the first 2 characters of a string

my_string="hola"
echo ${my_string:0:2}

Get the last 2 characters of a string

echo ${my_string: -2}

Remove the first character of a string

echo ${my_string:1}

Remove the last 2 characters of a string

echo ${my_string%??}

Display the first line where a pattern is found (here dim3), and remove the first characters that matches a given string

fslhd t1w.nii.gz | grep -m 1 dim3 | sed -e "s/^dim3           //"

Batch actions with grep

`grep` is powerful for creating an action based on a series of input (e.g. multiple files). Below is an example to delete several branches in git, based on their prefix name:

git branch -D `git branch | grep -E 'BRANCH_PREFIX*'`

Check if substring is in string

my_string='My long string'
if [[ $my_string == *"My long"* ]]; then
  echo "It's there!"
fi

More info here: http://tldp.org/LDP/abs/html/string-manipulation.html

Dates#

To list the date every week for the next five weeks, starting in 2 days:

for i in {1..5}; do echo $(date -v +${i}w -v +2d "+%Y-%m-%d"); done

FOR Loop#

Loop across list elements

ARRAY=(element1 element2 element3)
for i in ${ARRAY[@]}; do
  echo $i
done

Loop across list elements (using indices)

ARRAY=(element1 element2 element3)
for i in ${!ARRAY[@]}; do
  echo "Element: $((i+1))/${#ARRAY[@]}"
  echo ${ARRAY[$i]}
done

**Loop across numerical range (with zero filling)

START=30
END=150

for i in $(seq -f "%03g" $START $END); do
  echo $i
done

Loop across an array of strings

SUBJECT_LIST=(subject_a subject_b)

for subject in ${SUBJECT_LIST[@]}; do
  echo $subject
done

Loop across a series of files

for filename in im1 im2 im3 ; do
  bet $filename ${filename}_brain ;
done

Using ls

FILES=`ls folder/*.nii`
for file in $FILES; do
  echo $file
done

Do it in a single line:

FILES=`ls folder/*.nii`; for file in $FILES; do echo $file; done

Using find (recursive)

FILES=`find . -name *.nii`; for file in $FILES; do echo $file; done

IF Statements#

IF - AND#

if [ ! -z "$var" ] && [ -e "$var" ]; then
  do something ...
else
  do something else...
fi

alternative:

[ ! -z "$var" -a  -e "$var" ]

IF - OR#

if [[ "$s1" == "$s2" ]]; then
  do something...
fi

if [ ! -z "$var" ] || [ -e "$var" ]; then
  do something ...
fi

alternative:

[ ! -z "$var" -o  -e "$var" ]

CSV Files#

Parse CSV File#

while IFS=, read col1 col2 col3 col4 col5
  do
    echo "$col2"
  done < <FILE>.csv

Command Line Input#

#!/bin/bash
# use predefined variables to access passed arguments
# echo arguments to the shell
echo $1 $2 $3 ' -> echo $1 $2 $3'
# list all arguments:
echo $@

# We can also store arguments from bash command line in special array
args=("$@")
# echo arguments to the shell
echo ${args[0]} ${args[1]} ${args[2]} ' -> args=("$@"); echo ${args[0]} ${args[1]} ${args[2]}'

# use $@ to print out all arguments at once
echo $@ ' -> echo $@'

# use $# variable to print out number of arguments passed to the bash script
echo Number of arguments passed: $# ' -> echo Number of arguments passed: $#'

also see: Bash: parsing arguments with ‘getopts’

Log Files#

Generate log file #

LOGFILE=<FILE_NAME>.log
{
    # bash commands...
    
} 2>&1 | tee $LOGFILE

Generate a log file of a script directly in terminal:

script.$$ [options] | tee <FILE_NAME>.log

Add date to log file: log_file_name_$(date +%Y%m%d).logEdit

Colors#

The Mountain Lion Terminal does not support the command echo -e therefore the following has to be used:

printf "\e[0;32mText here\e[0m"

ANSI Escape Codes for Colours#

Colour

ANSI Escape Code

Black

0;30

Red

0;31

Green

0;32

Brown/Orange

0;33

Blue

0;34

Purple

0;35

Cyan

0;36

Light Grey

0;37

Yellow

1;33

White

1;37

No Colour

0

 
BLACK='\033[0;30m'
RED='\033[0;31m'
NC='\033[0m'

Misc#

Pass argument from file

mycommand "$(< file.txt)"

Test existence of a file

if [ -e "$var" ]; then