Linux Programming

Shell Programming

Some resource

• http://learnshell.org/

Redirect

Redirecting output. File descriptor number 1 (2) means standard output (error).

./myProgram > stdout.txt        # redirect std out to <stdout.txt>
./myProgram 2> stderr.txt       # redirect std err to <stderr.txt> by using the 2> operator
./myProgram > stdout.txt 2> stderr.txt # combination of above two
./myProgram > stdout.txt 2>&1   # redirect std err to std out <stdout.txt>
./myProgram >& /dev/null        # prevent writing std out and std err to the screen
ps >> outptu.txt                # append

Redirecting input

./myProgram < input.txt

>&

&> file is not part of the official POSIX shell spec, but has been added to many Bourne shells as a convenience extension (it originally comes from csh). In a portable shell script (and if you don't need portability, why are you writing a shell script?), use > file 2>&1 only.

tee

To redirect to both a file and the screen the same time, use tee command. See

• http://www.cyberciti.biz/faq/linux-redirect-error-output-to-file/
• https://en.wikipedia.org/wiki/Tee_(command)

Pipe

The operator is |.

ps > psout.txt
sort psout.txt > pssort.out

can be simplified to

ps | sort > pssort.out

For example,

$ head /etc/passwd
root:x:0:0:root:/root:/bin/bash
daemon:x:1:1:daemon:/usr/sbin:/bin/sh
bin:x:2:2:bin:/bin:/bin/sh
sys:x:3:3:sys:/dev:/bin/sh
sync:x:4:65534:sync:/bin:/bin/sync

$cat /etc/passwd | cut -d: -f7 | sort | uniq -c | sort -nr
     18 /bin/sh
     13 /bin/false
      2 /bin/bash
      1 /bin/sync

where cut command will extract the 7th field separated by the : character and write to the output stream. sort command will sort alphabetically sorts the line it reads from its input and returns the new sort to its output. The uniq command will remove and count duplicated lines. The final sort command will sort its input numerically in reverse order.

Pipe vs redirect

• Pipe is used to pass output to another program or utility.
• Redirect is used to pass output to either a file or stream.

In other words, thing1 | thing2 does the same thing as thing1 > temp_file && thing2 < temp_file.

Shebang (#!)

A shebang is the character sequence consisting of the characters number sign and exclamation mark (that is, "#!") at the beginning of a script. See the Wikipedia page.

The syntax looks like

#! interpreter [optional-arg]

For example,

• #!/bin/sh — Execute the file using sh, the Bourne shell, or a compatible shell
• #!/bin/csh -f — Execute the file using csh, the C shell, or a compatible shell, and suppress the execution of the user’s .cshrc file on startup
• #!/usr/bin/perl -T — Execute using Perl with the option for taint checks

Variables

food=Banana
echo $food
food="Apple"
echo $food

Environment variables

$HOME
$PATH
$0 -- name of the shell script
$# -- number of parameters passed
$$ process ID of the shell script, often used inside a script for generating unique temp filenames
$? -- the exit value of the last run command

For example,

#!/bin/sh
/usr/local/bin/my-command
if [ "$?" -ne "0" ]; then
  echo "Sorry, we had a problem there!"
fi

Parameter variables

$1, $2, .... -- parameters given to the script
$* -- list of all the parameters, in a single variable
$@ -- subtle variation on $*. 
$! -- the process id of the last command run in the background.

For example,

$ touch /tmp/tmpfile_$$

$ set foo bar bam
$ echo $#
3
$ echo $@
foo bar bam
$ set foo bar bam &
[1] 28212
$ echo $!
28212
[1]+  Done                    set foo bar bam

We can also use parentheses around the variable name.

QT_ARCH=x86_64
QT_SDK_BINARY=QtSDK-4.8.0-${QT_ARCH}.tar.gz
QT_SD_URL=https://xxx.com/$QT_SDK_BINARY

Conditions

We can use the test command to check if a file exists. The command is test -f <filename>.

[] is just the same as writing test, and would always leave a space after the test word.

if test -f fred.c; then ...; fi

if [ -f fred.c ]
then
...
fi

if [ -f fred.c ]; then
...
fi

Arithmetic comparison

expr1 -eq expr2  ==> check equal
expr1 -ne expr2  ==> check not equal
expr1 -gt expr2  ==> expr1 > expr2
expr1 -ge expr2  ==> expr1 >= expr2
expr1 -lt expr2  ==> expr1 < expr2
expr1 -le expr2  ==> expr1 <= expr2
! expr  ==> opposite of expr

File conditionals

-d file  ==> True if the file is a directory
-e file  ==> True if the file exists
-f file  ==> True if the file is a regular file
-r file  ==> True if the file is readable
-s file  ==> True if the file has non-zero size
-w file  ==> True if the file is writable
-x file  ==> True if the file is executable

Example: Suppose we want to know if the first argument (if given) match a specific string. We can use (note the space before and after '==')

#!/bin/bash
if [ $1 == "console" ]; then
  echo 'Console'
else
  echo 'Non-console'
fi

Control Structures

if

if condition
then
  statements
elif [ condition ]; then
  statements
else 
  statements
fi

For example, we can run a cp command if two files are different.

if ! cmp -s "$filesrc" "$filecur"
then
     cp $filesrc $filecur
fi

while

while condition do
  statements
done

until

until condition
do 
  statements
done

AND list

statement1 && statement2 && statement3 && ...

If command1 finishes successfully then run command2.

OR list

statement1 || statement2 || statement3 || ...

If command1 fails then run command2.

for

for variable in values
do 
  statements
done

Example 1

To convert pdfs to tifs using ImageMagick (for looping over files, check cyberciti.biz)

outdir="../plosone"
indir="../fig"

if [[ ! -d  $outdir ]];
then
   mkdir $outdir
fi

in=(file1.pdf file2.pdf file3.pdf)

for (( i=0; i<${#in[@]} ; i++ ))
do
  convert -strip -units PixelsPerInch -density 300 -resample 300 \
          -alpha off -colorspace RGB -depth 8 -trim -bordercolor white \
          -border 1% -resize '2049x2758>' -resize '980x980<' +repage \
          -compress lzw $indir/${in[$i]} $outdir/Figure$[$i+1].tiff
done

Example 2

A second example is to download all the (Ontario gasoline price) data with wget and parsing and concatenating the data with other *nix tools like 'sed':

# Download data
for i in $(seq 1990 2014)
        do wget http://www.energy.gov.on.ca/fuelupload/ONTREG$i.csv
done

# Retain the header
head -n 2 ONTREG1990.csv | sed 1d > ONTREG_merged.csv

# Loop over the files and use sed to extract the relevant lines
for i in $(seq 1990 2014)
        do
        tail -n 15 ONTREG$i.csv | sed 13,15d | sed 's/./-01-'$i',/4' >> ONTREG_merged.csv
        done

Example 3

Download all 20 sra files (60GB in total) from SRP032789.

for x in $(seq 1027175 1027180) 
   do wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP032/SRP032789/SRR$x/SRR$x.sra
done

Example 4

Convert all files from DOS to Unix format

for f in *.txt; do   tr -d '\r' < $f > tmp.txt;   mv tmp.txt $f  ; done
# Or
for file in $*; do   tr -d '\r' < $f > tmp.txt;   mv tmp.txt $f  ; done

Example 5

Include all files in a directory

for f in /etc/*.conf
do
   echo "$f"
done

Commands

break  ==> escaping from an enclosing for, while or until loop
:      ==> null command
continue ==> make the enclosing for, while or until loo continue at the next iteration
.      ==> executes the command in the current shell
eval   ==> evaluate arguments
exec   ==> replacing the current shell with a different program
export ==> make the variable named as its parameter available in subshells
expr   ==> evaluate its arguments as an expression
printf ==> similar to echo
set    ==> sets the parameter variables for the shell. Useful for using fields in commands that output spaced-separated values
shift  ==> moves all the parameter variables down by one.
trap   ==> specify the actions to take on receipt of signals.
unset  ==> remove variables or functions from the environment.

set -e: Exit immediately if a command exits with a non-zero status. Type help set in command line. See stackoverflow.com

trap

• http://www.computerhope.com/unix/utrap.htm
• http://linuxcommand.org/wss0160.php
• http://www.tutorialspoint.com/unix/unix-signals-traps.htm
• http://www.ibm.com/developerworks/aix/library/au-usingtraps/
• http://bash.cyberciti.biz/guide/Trap_statement
• http://steve-parker.org/sh/trap.shtml (trap with a user-defined function)
• http://www.turnkeylinux.org/blog/shell-error-handling (set -e)
• http://unix.stackexchange.com/questions/17314/what-is-signal-0-in-a-trap-command (do something on EXIT)
• http://unix.stackexchange.com/questions/79648/how-to-trigger-error-using-trap-command

The syntax to use trap command is

trap command signal

For example,

$ cat traptest.sh
#!/bin/sh

trap 'rm -f /tmp/tmp_file_$$' INT
echo creating file /tmp/tmp_file_$$
date > /tmp/tmp_file_$$

echo 'press interrupt to interrupt ...'
while [ -f /tmp/tmp_file_$$ ]; do
  echo file exists
  sleep 1
done
echo the file no longer exists

trap - INT
echo creaing file /tmp/tmp_file_$$
date > /tmp/tmp_file_$$
echo 'press interrupt to interrupt ...'
while [ -f /tmp/tmp_file_$$ ]; do
  echo file exists
  sleep 1
done
echo we never get here
exit 0

will get an output like

$ ./traptest.sh
creating file /tmp/tmp_file_21389
press interrupt to interrupt ...
file exists
file exists
^Cthe file no longer exists
creaing file /tmp/tmp_file_21389
press interrupt to interrupt ...
file exists
file exists
^C

The first when we use trap, it will delete the file when we hit Ctrl+C. The second time when we use trap, we do not specify any command to be exected when an INT signal occurs. So the default behavior occurs. That is, the final echo and exit statements are never executed.

Note that the following two are different.

trap - INT
trap '' INT

The second command will IGNORE signals (Ctrl+C in this case) so if we apply this statement above, we will not be able to use Ctrl+C to kill the execution.

Command Execution

$(command)
`command`    # ` is a backquote/backtick, not a single quotation sign
# Example
sudo apt-get install linux-headers-$(uname -r)

Note all new scripts should use the $(...) form, which was introduced to avoid some rather complex rules.

Example

#!/bin/sh
echo The current directory is $PWD
echo The current users are $(who)
sudo chown `id -u` SomeDir  # change the ownership to the current user. Dangerous!
                            # Or sudo chown `whoami` SomeDirOrSomeFile
exit 0

Note that $(your expression) is a better way as it allows you to run nest expressions. For example,

cd $(dirname $(type -P touch))

will cd you into the directory containing the 'touch' command.

The concept of putting the result of a command into a script variable is very powerful, as it makes it easy to use existing commands in scripts and capture their output.

Arithmetic Expansion

$((...))

is a better alternative to the expr command. More examples:

for i in $(seq 1 3)
  do echo SRR$(( i + 1027170 ))'_1'.fastq 
done

Note that the single quote above is required. The above will output SRR1027171_1.fastq, SRR102172_1.fastq and SRR1027173_1.fastq.

Parameter Expansion

${parameter}

Bash shell find out if a command exists or not

http://www.cyberciti.biz/faq/unix-linux-shell-find-out-posixcommand-exists-or-not/

POSIX command

# command -v will return >0 when the command1 is not found
command -v command1 >/dev/null && echo "command1 Found In \$PATH" || echo "command1 Not Found in \$PATH"

$ help command
command: command [-pVv] command [arg ...]
    Execute a simple command or display information about commands.
    
    Runs COMMAND with ARGS suppressing  shell function lookup, or display
    information about the specified COMMANDs.  Can be used to invoke commands
    on disk when a function with the same name exists.
    
    Options:
      -p	use a default value for PATH that is guaranteed to find all of
    	the standard utilities
      -v	print a description of COMMAND similar to the `type' builtin
      -V	print a more verbose description of each COMMAND
    
    Exit Status:
    Returns exit status of COMMAND, or failure if COMMAND is not found.

type -P

type -P command1 &>/dev/null && echo "Found" || echo "Not Found"

$ help type
type: type [-afptP] name [name ...]
    Display information about command type.
    
    For each NAME, indicate how it would be interpreted if used as a
    command name.
    
    Options:
      -a	display all locations containing an executable named NAME;
    	includes aliases, builtins, and functions, if and only if
    	the `-p' option is not also used
      -f	suppress shell function lookup
      -P	force a PATH search for each NAME, even if it is an alias,
    	builtin, or function, and returns the name of the disk file
    	that would be executed
      -p	returns either the name of the disk file that would be executed,
    	or nothing if `type -t NAME' would not return `file'.
      -t	output a single word which is one of `alias', `keyword',
    	`function', `builtin', `file' or `', if NAME is an alias, shell
    	reserved word, shell function, shell builtin, disk file, or not
    	found, respectively
    
    Arguments:
      NAME	Command name to be interpreted.
    
    Exit Status:
    Returns success if all of the NAMEs are found; fails if any are not found.
typeset: typeset [-aAfFgilrtux] [-p] name[=value] ...
    Set variable values and attributes.
    
    Obsolete.  See `help declare'.

pause by read -p command

http://www.cyberciti.biz/tips/linux-unix-pause-command.html

read -p "Press [Enter] key to start backup..."

If we want to ask users about a yes/no question, we can use this method

while true; do
    read -p "Do you wish to install this program? " yn
    case $yn in
        [Yy]* ) make install; break;;
        [Nn]* ) exit;;
        * ) echo "Please answer yes or no.";;
    esac
done

OR

echo "Do you wish to install this program?"
select yn in "Yes" "No"; do
    case $yn in
        Yes ) make install; break;;
        No ) exit;;
    esac
done

Keyboard input and Arithmetic

http://linuxcommand.org/wss0110.php

read

#!/bin/bash

echo -n "Enter some text > "
read text
echo "You entered: $text"

Arithmetic

#!/bin/bash

# An applications of the simple command
# echo $((2+2))
# That is, when you surround an arithmetic expression with the double parentheses, 
# the shell will perform arithmetic evaluation.
first_num=0
second_num=0

echo -n "Enter the first number --> "
read first_num
echo -n "Enter the second number -> "
read second_num

echo "first number + second number = $((first_num + second_num))"
echo "first number - second number = $((first_num - second_num))"
echo "first number * second number = $((first_num * second_num))"
echo "first number / second number = $((first_num / second_num))"
echo "first number % second number = $((first_num % second_num))"
echo "first number raised to the"
echo "power of the second number   = $((first_num ** second_num))"

and a program that formats an arbitrary number of seconds into hours and minutes:

#!/bin/bash

seconds=0

echo -n "Enter number of seconds > "
read seconds

# use the division operator to get the quotient
hours=$((seconds / 3600))
# use the modulo operator to get the remainder
seconds=$((seconds % 3600))
minutes=$((seconds / 60))
seconds=$((seconds % 60))

echo "$hours hour(s) $minutes minute(s) $seconds second(s)"

Debugging Scripts

http://www.cyberciti.biz/tips/debugging-shell-script.html

• Run a shell script with -x option. Then each lines of the script will be shown on the stdout. We can see which line takes long time or which lines broke the code (it still runs through the script).

$ bash -x script-name

• Use of set builtin command
• Use of intelligent DEBUG function

To run a bash script line by line:

• Bash Debugger
• Use Geany. Select a region of code. Edit -> >Commands->Send selection to Terminal. You can also assign a keybinding for this. To do so: go to Edit->Preferences and pick the Keybindings tab.

$ tmpname=$(basename $inputVCF)
Command 'basename' is available in '/usr/bin/basename'
The command could not be located because '/usr/bin' is not included in the PATH environment variable.

Examples

• <upgrade8.sh> file from BioLinux installation page

Text processing

Extract columns from text files: cut

http://www.thegeekstuff.com/2013/06/cut-command-examples/

To extract fixed columns (say columns 5-7 of a file):

cut -c5-7 somefile

If the field delimiter is different from TAB you need to specify it using -d:

cut -d' ' -f100-105 myfile > outfile
#
cut -d: -f6 somefile   # colon-delimited file
# 
grep "/bin/bash" /etc/passwd | cut -d':' -f1-4,6,7    # field 1 through 4, 6 and 7

Extract columns from text files: awk

awk -F : '{print $6}' somefile   # colon-delimited file
#
awk --field-searator="\\t" '{print $6}' filename    # tab-delimited
# 
awk -F":" '{ print $1 " " $3 }' /etc/passwd

Substitution of text: sed (stream editor)

• https://en.wikipedia.org/wiki/Sed
• Append, Insert, Replace, and Count File Lines

Substitution of text: perl

• Add or remove 'chr' from vcf file https://www.biostars.org/p/18530/

How to wrap a long linux command

Use backslash character. However, make sure the backslash character is the last character at a line. For example the first example below does not work since there is an extra space character after \.

Example 1 (not work)

sudo apt-get install libcap-dev libbz2-dev libgcrypt11-dev libpci-dev libnss3-dev libxcursor-dev \
   libxcomposite-dev libxdamage-dev libxrandr-dev libdrm-dev libfontconfig1-dev libxtst-dev \ 
   libcups2-dev libpulse-dev libudev-dev

vs example 2 (work)

sudo apt-get install libcap-dev libbz2-dev libgcrypt11-dev libpci-dev libnss3-dev libxcursor-dev \
   libxcomposite-dev libxdamage-dev libxrandr-dev libdrm-dev libfontconfig1-dev libxtst-dev \
   libcups2-dev libpulse-dev libudev-dev

Working with Files

Low-level File Access

• file descriptors: 0 means standard input, 1 means standard output, 2 means standard error.
• size_t write(int fildes, const void *buf, size_t nbytes);

#include <unistd.h>
#include <stdlib.h>
int main()
{
  if ((write(1, "Here is some data\n", 18)) != 17)
    write(2, "A write error has occurred on file descriptor\n", 46);
  exit(0);
}

• size_t read(int fildes, void *buf, size_t nbytes); returns the number of data bytes actually read. If a read call returns 0, it had nothing to read; it reached the end of the file. An error on the call will cause it to return -1.
• To create a new file descriptor we use the open system call. int open(const char *path, int oflags, mode_t mode);

• The next program will do file copy.

#include <unistd.h>
#include <sys/stat.h>
#include <fcntl.h>
#include <stdlib.h>
int main()
{
  char c;
  int in, out;
  in = open("file.in", O_RDONLY);
  out = open("file.out", O_WRONLY|O_CREAT, S_IRUSER|S_IWUSR);
  while(read(in,&c,1) == 1)
    write(out,&c,1)
  exit(0);
}

The Standard I/O Library

• fopen, fclose
• fread, fwrite
• fflush
• fseek
• fgetc, getc, getchar
• fputc, putc, putchar
• fgets, gets
• printf, fprintf and sprintf
• scanf, fscanf and sscanf

Formatted Input and Output

• prinf, fprintf and sprintf
• scanf, fscanf and sscanf

Stream Errors

• How do You Run a Command in the Background with No Output Unless There is an Error?

Scanning Directories

• opendir, closedir
• readdir
• telldir
• seekdir

Curses

A technique between command line and full GUI.

Example: vi.

Development Tools

make and Makefiles

• minimal make A minimal tutorial on make from Karl Broman.
• http://makefiletutorial.com/index.html