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Basic Programming in Bash

This document provides an introduction to basic Bash programming and scripting. It explains how to write simple Bash scripts using variables, conditionals, and loops to automate tasks. As an example, it walks through a Bash workflow script used by the MMseqs2 software to perform taxonomic classification through a series of steps calling both Bash commands and MMseqs2 programs. Exercises provided practice writing Bash scripts to compute sums, check user input, and iterate commands.

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jona
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8 views

Basic Programming in Bash

This document provides an introduction to basic Bash programming and scripting. It explains how to write simple Bash scripts using variables, conditionals, and loops to automate tasks. As an example, it walks through a Bash workflow script used by the MMseqs2 software to perform taxonomic classification through a series of steps calling both Bash commands and MMseqs2 programs. Exercises provided practice writing Bash scripts to compute sums, check user input, and iterate commands.

Uploaded by

jona
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Basic programming in Bash

Bash programming
• In the previous tutorial you got to know basic Bash commands
• Bash is also a programming (scripting) language
• More sophisticated execution of commands (upon a condition,
several times in a row, etc.) is possible through Bash scripts
Motivation
• Basic programming is useful as it allows you to automate tasks
• MMseqs2 software suite allows creating tailored computational tools
by combining its modules and workflows in Bash scripts

createdb createdb

taxonomy search

filterdb filterdb

search
The script file
• The first line of a Bash script is usually:
#!/bin/bash
• This indicates this file is a Bash script
• Lines that start with ‘#’ are comments
• To print something we use ‘echo’
• A script is just a text file.
• Under your home directory, create a directory called “Bash_scripts”
• We will create Bash scripts there
Creating the Hello_Bash.sh script file
Running a Bash script
• You need to give your script execution permission:
chmod +x ~/Bash_scripts/Hello_Bash.sh
• Then you can run it from the terminal:
Hello_Bash.sh
Create a Hello_Bash.sh script and run it
Bash variables
• A variable stores a value
• There are no variable types in Bash
• Assignment of a value is done with “=“:

#!/bin/bash
NAME="Eli"
NUMBER_OF_EYES=3
echo "Hello $NAME, you have $NUMBER_OF_EYES eyes"

• Modify the Hello_Bash.sh script to have a variable and run it


Arithmetic evaluation
• In order for bash to treat the variable as numeric we need to use
brackets:

CORRECT_NUMBER_OF_EYES=$((NUMBER_OF_EYES – 1))
echo "Humans usually don't have more than
$CORRECT_NUMBER_OF_EYES eyes"

• Create a Bash script with a variable AGE and assign it your age. Print
the age you will be in one year
Conditionals
• If/else structures allow us to execute commands only in certain cases

AGE=20
if [ "$AGE" -eq 20 ]; then
echo "Wow, you are exactly 20!"
fi Description Numeric String
less than -lt <
greater than -gt >
• Comparison operators:
equal -eq =
not equal -ne !=
less or equal -le
greater or equal -ge
Exercise
• This simple Bash script asks the user for their name and says hi:

#!/bin/bash
echo "Enter your name and press [ENTER]: "
read NAME
echo "Hi $NAME"

• Create a script that asks for the user’s age and serves beer only if
the user is at least 18
What does this code do?
echo "Enter a directory name and press [ENTER]: "
read DIR
if [ -d "$DIR" ]; then
ls "$DIR"
else
mkdir "$DIR"
fi
Repetitive execution of commands
• Often we would like to perform the same thing more than once:
• Say hello to all students in the class (there 22 of you!)
• Make a copy of each file in a directory
• Refine an MMseqs2 clustering…

• Bash loops allow us to do exactly that!


For loop
#!/bin/bash
START=1
END=22
for (( i=$START; i<=$END; i++ ))
do
echo "$i. Hi, student!"
done
While loop
# continue from last slide
i=1
while [[ $i -le $END ]]
do
echo "$i. Oh hi there, student!"
((i = i + 1))
done
Exercises
1. Compute the sum of the first 40 natural numbers:
1+2+…

2. Sum the numbers the user provides you until they provide a
negative number

Can you tell how many numbers you summed?


Taxonomy Bash workflow
• In the previous tutorial you saw MMseqs2 workflow to assign
taxonomic units.
• This workflow is written as a Bash script which calls Bash commands
as well as MMseqs2 native CPP modules
• Let’s have a look…
Taxonomy Bash workflow
INPUT="$1"
TARGET="$2"
RESULTS="$3"
TMP_PATH="$4"

if [ ! -e "${TMP_PATH}/first" ]; then
"$MMSEQS" search "${INPUT}" "${TARGET}" "${TMP_PATH}/first"
"${TMP_PATH}/tmp_hsp1" ${SEARCH1_PAR} \
|| fail "First search died"
fi

if [ ! -e "${TMP_PATH}/top1" ]; then
"$MMSEQS" filterdb "${TMP_PATH}/first" "${TMP_PATH}/top1" --extract-lines 1 \
|| fail "Filterdb died"
fi
Taxonomy Bash workflow
if [ ! -e "${TMP_PATH}/aligned" ]; then
"$MMSEQS" extractalignedregion "${INPUT}" "${TARGET}" "${TMP_PATH}/top1"
"${TMP_PATH}/aligned" --extract-mode 2 \
|| fail "Extractalignedregion failed"
fi

if [ ! -e "${TMP_PATH}/round2" ]; then
"$MMSEQS" search "${TMP_PATH}/aligned" "${TARGET}" "${TMP_PATH}/round2"
"${TMP_PATH}/tmp_hsp2" ${SEARCH2_PAR} \
|| fail "Second search died"
fi
Taxonomy Bash workflow
# Concat top hit from 1st search with all results from 2nd search
if [ ! -e "${TMP_PATH}/merged" ]; then
"$MMSEQS" mergedbs "${TMP_PATH}/top1" "${TMP_PATH}/merged" "${TMP_PATH}/top1"
"${TMP_PATH}/round2" \
|| fail "Mergedbs died"
fi

# Filter out 2nd search entries that do not reach the evalue of the top 1 hit
if [ ! -e "${TMP_PATH}/2b_ali" ]; then
"$MMSEQS" filterdb "${TMP_PATH}/merged" "${TMP_PATH}/2b_ali" --beats-first --
filter-column 4 --comparison-operator le \
|| fail "First filterdb died"
fi

"$MMSEQS" lca "${TARGET}" "${TMP_PATH}/2b_ali" "${RESULTS}" ${LCA_PAR} \


|| fail "Lca died"
Exercise solutions
#!/bin/bash
echo "Hello Bash"
Exercise solutions
#!/bin/bash
AGE=99
AGE_NEXT_YEAR=$((AGE + 1))
echo "Next year you will be $AGE_NEXT_YEAR"
Exercise solutions
#!/bin/bash
echo "Enter your age and press [ENTER]: "
read USER_AGE
if [ $USER_AGE -ge 18 ]; then
echo "Here is your beer"
fi
Exercise solutions
#!/bin/bash
START=1
END=40
SUM=0
for ((i=$START; i<=$END; i++)) do
SUM=$((SUM+i))
done
echo "The result is $SUM"
Exercise solutions
#!/bin/bash
USER_NUMBER=0
NUM_NUMBERS=-1
SUM=0
while [[ $USER_NUMBER -ge 0 ]]
do
SUM=$((SUM+USER_NUMBER))
NUM_NUMBERS=$((NUM_NUMBERS+1))
echo "Insert a new number [negative number to exit]:"
read USER_NUMBER
done
echo "Final sum is $SUM and $NUM_NUMBERS numbers were summed"

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