9  Batch processing

Objective: Learn basics of batch processing in GNU/Linux

In the previous section, we have seen how to handle streams and text. We can use this knowledge to generate list of command instead of text. This is called batch processing.

In everyday life, you may want to run command sequentiality without using pipes.

To run CMD1 and then run CMD2 you can use the ; operator

CMD1 ; CMD2

To run CMD1 and then run CMD2 if CMD1 didn’t throw an error, you can use the && operator which is safer than the ; operator.

CMD1 && CMD2

You can also use the || to manage errors and run CMD2 if CMD1 failed.

CMD1 || CMD2

9.1 Executing list of commands

The easiest option to execute list of command is to use xargs. xargs reads arguments from stdin and use them as arguments for a command. In UNIX systems the command echo send string of character into stdout. We are going to use this command to learn more about xargs.

echo "hello world"

In general a string of character differs from a command when it’s placed between quotes.

The two following commands are equivalent, why ?

echo "file1 file2 file3" | xargs touch
touch file1 file2 file3

You can display the command executed by xargs with the switch -t.

By default the number of arguments sent by xargs is defined by the system. You can change it with the option -n N, where N is the number of arguments sent. Use the option -t and -n to run the previous command as 3 separate touch commands.

Solution

echo "file1 file2 file3" | xargs -t -n 1 touch

Sometime, the arguments are not separated by space but by other characters. You can use the -d option to specify them. Execute touch1 time from the following command:

echo "file1;file2;file3"

Solution

echo "file1;file2;file3" | xargs -t -d \; touch

To reuse the arguments sent to xargs you can use the command -I which defines a string corresponding to the argument. Try the following command, what does the manual says about the -c option of the command cut ?

ls -l file* | cut -c 44- | xargs -t -I % ln -s % link_%

Instead of using ls the command xargs is often used with the command find. The command find is a powerful command to search for files.

Modify the following command to make a non-hidden copy of all the file with a name starting with .bash in your home folder

find . -name ".bash*" | sed 's|./.||g'

Solution

find . -name ".bash*" | sed 's|./.||g' | xargs -t -I % cp .% %

You can try to remove all the files in the /tmp folder with the following command:

find /tmp/ -type f | xargs -t rm

Modify this command to remove every folder in the /tmp folder.

Solution

find /tmp/ -type d | xargs -t rm -R

9.2 Writing awk commands

xargs It is a simple solution for writing batch commands, but if you want to write more complex command you are going to need to learn awk. awk is a programming language by itself, but you don’t need to know everything about awk to use it.

You can to think of awk as a xargs -I $N command where $1 correspond to the first column $2 to the second column, etc.

There are also some predefined variables that you can use like.

• $0 Correspond to all the columns.
• FS the field separator used
• NF the number of fields separated by FS
• NR the number of records already read

A awk program is a chain of commands with the form motif { action }

• the motif define where there action is executed
• there action is what you want to do

They motif can be

• a regexp
• The keyword BEGINor END (before reading the first line, and after reading the last line)
• a comparison like <, <=, ==, >=, > or !=
• a combination of the three separated by && (AND), ||(OR) and ! (Negation)
• a range of line motif_1,motif_2

With awk you can

Count the number of lines in a file

awk '{ print NR " : " $0 }' file

Modify this command to only display the total number of line with awk (like wc -l)

Solution

awk 'END{ print NR }' file

Convert a tabulated sequences file into fasta format

awk -vOFS='' '{print ">",$1,"\n",$2,"\n";}' two_column_sample_tab.txt > sample1.fa

Modify this command to only get a list of sequence names in a fasta file

Solution

awk -vOFS='' '{print $1 "\n";}' two_column_sample_tab.txt > seq_name.txt

Convert a multiline fasta file into a single line fasta file

awk '!/^>/ { printf "%s", $0; n = "\n" } /^>/ { print n $0; n = "" } END { printf "%s", n }' sample.fa > sample1_singleline.fa

Convert fasta sequences to uppercase

awk '/^>/ {print($0)}; /^[^>]/ {print(toupper($0))}' file.fasta > file_upper.fasta

Modify this command to only get a list of sequence names in a fasta file un lowercase

Solution

awk '/[^>]/ {print(tolower($0))}' file.fasta > seq_name_lower.txt

Return a list of sequence_id sequence_length from a fasta file

awk 'BEGIN {OFS = "\n"}; /^>/ {print(substr(sequence_id, 2)" "sequence_length); sequence_length = 0; sequence_id = $0}; /^[^>]/ {sequence_length += length($0)}; END {print(substr(sequence_id, 2)" "sequence_length)}' file.fasta

Count the number of bases in a fastq.gz file

(gzip -dc $0) | awk 'NR%4 == 2 {basenumber += length($0)} END {print basenumber}'

Only read with more than 20bp from a fastq

awk 'BEGIN {OFS = "\n"} {header = $0 ; getline seq ; getline qheader ; getline qseq ; if (length(seq) >= 20){print header, seq, qheader, qseq}}' < input.fastq > output.fastq

9.3 Writing a bash script

When you start writing complicated command, you may want to save them to reuse them later.

You can find everything that you are typing in your bashin the ~/.bash_history file, but working with this file can be tedious as it also contains all the command that you mistype. A good solution, for reproducibility is to write bash scripts. A bash script is simply a text file that contains a sequence of bashcommands.

As you use bash in your terminal, you can execute a bash script with the following command:

source myscrip.sh

It’s usual to write the .sh extension for shellscripts.

Write a bash script named download_hg38.sh that download the hg38.ncbiRefSeq.gtf.gz file, then extract it and that says that it has done it.

The \ character like in regexp cancel the meaning of what follow, you can use it to split your one-liner scripts over many lines to use the && operator.

Solution

wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/hg38.ncbiRefSeq.gtf.gz && \
gzip -dc hg38.ncbiRefSeq.gtf.gz && \
echo "download and extraction complete"

9.3.1 shebang

In your first bash script, the only thing saying that your script is a bash script is its extension. But most of the time UNIX system doesn’t care about file extension, a text file is a text file.

To tell the system that your text file is a bash script you need to add a shebang. A shebang is a special first line that starts with a #! followed by the path of the interpreter for your script.

For example, for a bash script in a system where bash is installed in /bin/bash the shebang is:

##!/bin/bash

When you are not sure whichis the path of the tools available to interpret your script, you can use the following shebang:

##!/usr/bin/env bash

You can add a shebang to your script and add it the executable right.

Solution

chmod u+x download_hg38.sh

Now you can execute your script with the command:

./download_hg38.sh

Congratulations you wrote your first program !

9.3.2 PATH

Where did they /usr/bin/env find the information about your bash ? Why did we have to write a ./ before our script if we are in the same folder ?

This is all linked to the PATH bash variable. Like in many programming languages bash have what we call variables. variables are named storage for temporary information. You can print a list of all your environment variables (variables loaded in your bash memory), with the command printenv.

To create a new variable you can use the following syntax:

VAR_NAME="text"
VAR_NAME2=2

Create a IDENTIY variable with your first and last names.

Solution

IDENTITY="First name Last Name"

It’s good practice to write your bash variable in uppercase with _ in place of spaces.

You can access the value of an existing bash variable with the $VAR_NAME

To display the value of your IDENTITY variable with echo you can write:

echo $IDENTITY

When you want to mix variable value and text you can use the two following syntax:

echo "my name is "$IDENTITY
echo "my name is ${IDENTITY}"

Going back to the printenv You can see a PWD variable that store your current path, a SHELL variable that store your current shell, and you can see a PATH variable that stores a loot of file path separated by :.

The PATH variable contains every folder where to look for executable programs. Executable programs can be binary files or text files with a shebang.

Display the content of PATH with echo

Solution

echo $PATH

You can create a scriptsfolder and move your download_hg38.sh script in it. Then we can modify the PATH variable to include the scripts folder in it.

Don’t erase your PATH variable !

Solution

mkdir ~/scripts
mv `download_hg38.sh` ~/scripts/
PATH=$PATH:~/scripts/

You can check the result of your command with echo $PATH

Try to call your download_hg38.sh from anywhere on the file tree. Congratulation you installed your first UNIX program !

9.3.3 Arguments

You can pass argument to your bash scripts, writing the following command:

my_script.sh arg1 arg2 arg3

Means that from within the script:

• $0 will give you the name of the script (my_script.sh)
• $1, $2, $3, $n will give you the value of the arguments (arg1, arg2, arg3, argn)
• $$ the process id of the current shell
• $# the total number of arguments passed to the script
• $@the value of all the arguments passed to the script
• $? the exit status of the last executed command
• $!the process id of the last executed command

You can write the following variables.sh script in your scripts folder:

##!/bin/bash

echo "Name of the script: $0"
echo "Total number of arguments: $#"
echo "Values of all the arguments: $@"

And you can try to call it with some arguments !

We have used the following commands:

• echo to display text
• xarg to execute a chain of commands
• awk to execute complex chain of commands
• ; && and || to chain commands
• source to load a script
• shebang to specify the language of a script
• PATH to install script

In the next session, we are going to learn how to execute command on other computers with ssh.

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