More at https://www.raku.org/

Address of the bookmark: https://www.raku.org/

More at https://bioinformaticsonline.com/snippets/view/42919/perl-ipcopen2-module

2. exec””

 syntax: exec "command";

3. Backticks “ or qx//

syntax: `command`;

syntax: qx/command/;

4. IPC::Open3

syntax: $output = open3(\*CHLD_IN, \*CHLD_OUT, \*CHLD_ERR, 'command arg1 arg2', 'optarg',...);

It is very similar to IPC::Open2 with the capability to capture all three file handles of the process, i.e., STDIN, STDOUT, and STDERR. It can also be used with or without the shell. You can read about it more in the documentation: IPC::Open3.

$output = open3(my $o ut, my $in, 'command arg1 arg2');

OR without using the shell

$output = open3(my $out, my $in, 'command', 'arg1', 'arg2');

5.a2p

syntax: a2p [options] [awkscript]

There is a Perl utility known as a2p which translates awk command to Perl. It takes awk script as input and generates a comparable Perl script as the output. Suppose, you want to execute the following awk statement

awk '{$1 = ""; $2 = ""; print}' f1.txt

This statement gives error sometimes even after escaping the variables (\$1, \$2) but by using a2p it can be easily converted to Perl script:

For further information, you can read it’s documentation: a2p

More help at https://bioinformaticsonline.com/snippets/view/42920/perl-script-to-run-awk-inside-perl

6. system()

syntax: system( "command" );

It is also a Perl function (perlfunc) that executes a command and waits for it to get finished first and then resume the Perl script. The return value is the exit status of the command. It can be called in two ways:

system( "command arg1 arg2" );

OR

system( "command", "arg1", "arg2" );

HELP

Here are some useful Perl cheat sheets that can be used as a quick reference guide.-- https://www.pcwdld.com/perl-cheat-sheet

# Double space a file
perl -pe '$\="\n"'
perl -pe 'BEGIN { $\="\n" }'
perl -pe '$_ .= "\n"'
perl -pe 's/$/\n/'
perl -nE 'say'

# Double space a file, except the blank lines
perl -pe '$_ .= "\n" unless /^$/'
perl -pe '$_ .= "\n" if /\S/'

# Triple space a file
perl -pe '$\="\n\n"'
perl -pe '$_.="\n\n"'

# N-space a file
perl -pe '$_.="\n"x7'

# Add a blank line before every line
perl -pe 's//\n/'

# Remove all blank lines
perl -ne 'print unless /^$/'
perl -lne 'print if length'
perl -ne 'print if /\S/'

# Remove all consecutive blank lines, leaving just one
perl -00 -pe ''
perl -00pe0

# Compress/expand all blank lines into N consecutive ones
perl -00 -pe '$_.="\n"x4'

# Fold a file so that every set of 10 lines becomes one tab-separated line
perl -lpe '$\ = $. % 10 ? "\t" : "\n"'

LINE NUMBERING
--------------

# Number all lines in a file
perl -pe '$_ = "$. $_"'

# Number only non-empty lines in a file
perl -pe '$_ = ++$a." $_" if /./'

# Number and print only non-empty lines in a file (drop empty lines)
perl -ne 'print ++$a." $_" if /./'

# Number all lines but print line numbers only non-empty lines
perl -pe '$_ = "$. $_" if /./'

# Number only lines that match a pattern, print others unmodified
perl -pe '$_ = ++$a." $_" if /regex/'

# Number and print only lines that match a pattern
perl -ne 'print ++$a." $_" if /regex/'

# Number all lines, but print line numbers only for lines that match a pattern
perl -pe '$_ = "$. $_" if /regex/'

# Number all lines in a file using a custom format (emulate cat -n)
perl -ne 'printf "%-5d %s", $., $_'

# Print the total number of lines in a file (emulate wc -l)
perl -lne 'END { print $. }'
perl -le 'print $n=()=<>'
perl -le 'print scalar(()=<>)'
perl -le 'print scalar(@foo=<>)'
perl -ne '}{print $.'
perl -nE '}{say $.'

# Print the number of non-empty lines in a file
perl -le 'print scalar(grep{/./}<>)'
perl -le 'print ~~grep{/./}<>'
perl -le 'print~~grep/./,<>'
perl -E 'say~~grep/./,<>'

# Print the number of empty lines in a file
perl -lne '$a++ if /^$/; END {print $a+0}'
perl -le 'print scalar(grep{/^$/}<>)'
perl -le 'print ~~grep{/^$/}<>'
perl -E 'say~~grep{/^$/}<>'

# Print the number of lines in a file that match a pattern (emulate grep -c)
perl -lne '$a++ if /regex/; END {print $a+0}'
perl -nE '$a++ if /regex/; END {say $a+0}'

CALCULATIONS
------------

# Check if a number is a prime
perl -lne '(1x$_) !~ /^1?$|^(11+?)\1+$/ && print "$_ is prime"'

# Print the sum of all the fields on a line
perl -MList::Util=sum -alne 'print sum @F'

# Print the sum of all the fields on all lines
perl -MList::Util=sum -alne 'push @S,@F; END { print sum @S }'
perl -MList::Util=sum -alne '$s += sum @F; END { print $s }'

# Shuffle all fields on a line
perl -MList::Util=shuffle -alne 'print "@{[shuffle @F]}"'
perl -MList::Util=shuffle -alne 'print join " ", shuffle @F'

# Find the minimum element on a line
perl -MList::Util=min -alne 'print min @F'

# Find the minimum element over all the lines
perl -MList::Util=min -alne '@M = (@M, @F); END { print min @M }'
perl -MList::Util=min -alne '$min = min @F; $rmin = $min unless defined $rmin && $min > $rmin; END { print $rmin }'

# Find the maximum element on a line
perl -MList::Util=max -alne 'print max @F'

# Find the maximum element over all the lines
perl -MList::Util=max -alne '@M = (@M, @F); END { print max @M }'

# Replace each field with its absolute value
perl -alne 'print "@{[map { abs } @F]}"'

# Find the total number of fields (words) on each line
perl -alne 'print scalar @F'

# Print the total number of fields (words) on each line followed by the line
perl -alne 'print scalar @F, " $_"'

# Find the total number of fields (words) on all lines
perl -alne '$t += @F; END { print $t}'

# Print the total number of fields that match a pattern
perl -alne 'map { /regex/ && $t++ } @F; END { print $t }'
perl -alne '$t += /regex/ for @F; END { print $t }'
perl -alne '$t += grep /regex/, @F; END { print $t }'

# Print the total number of lines that match a pattern
perl -lne '/regex/ && $t++; END { print $t }'

# Print the number PI to n decimal places
perl -Mbignum=bpi -le 'print bpi(n)'

# Print the number PI to 39 decimal places
perl -Mbignum=PI -le 'print PI'

# Print the number E to n decimal places
perl -Mbignum=bexp -le 'print bexp(1,n+1)'

# Print the number E to 39 decimal places
perl -Mbignum=e -le 'print e'

# Print UNIX time (seconds since Jan 1, 1970, 00:00:00 UTC)
perl -le 'print time'

# Print GMT (Greenwich Mean Time) and local computer time
perl -le 'print scalar gmtime'
perl -le 'print scalar localtime'

# Print local computer time in H:M:S format
perl -le 'print join ":", (localtime)[2,1,0]'

# Print yesterday's date
perl -MPOSIX -le '@now = localtime; $now[3] -= 1; print scalar localtime mktime @now'

# Print date 14 months, 9 days and 7 seconds ago
perl -MPOSIX -le '@now = localtime; $now[0] -= 7; $now[4] -= 14; $now[7] -= 9; print scalar localtime mktime @now'

# Prepend timestamps to stdout (GMT, localtime)
tail -f logfile | perl -ne 'print scalar gmtime," ",$_'
tail -f logfile | perl -ne 'print scalar localtime," ",$_'

# Calculate factorial of 5
perl -MMath::BigInt -le 'print Math::BigInt->new(5)->bfac()'
perl -le '$f = 1; $f *= $_ for 1..5; print $f'

# Calculate greatest common divisor (GCM)
perl -MMath::BigInt=bgcd -le 'print bgcd(@list_of_numbers)'

# Calculate GCM of numbers 20 and 35 using Euclid's algorithm
perl -le '$n = 20; $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $m'

# Calculate least common multiple (LCM) of numbers 35, 20 and 8
perl -MMath::BigInt=blcm -le 'print blcm(35,20,8)'

# Calculate LCM of 20 and 35 using Euclid's formula: n*m/gcd(n,m)
perl -le '$a = $n = 20; $b = $m = 35; ($m,$n) = ($n,$m%$n) while $n; print $a*$b/$m'

# Generate 10 random numbers between 5 and 15 (excluding 15)
perl -le '$n=10; $min=5; $max=15; $, = " "; print map { int(rand($max-$min))+$min } 1..$n'

# Find and print all permutations of a list
perl -MAlgorithm::Permute -le '$l = [1,2,3,4,5]; $p = Algorithm::Permute->new($l); print @r while @r = $p->next'

# Generate the power set
perl -MList::PowerSet=powerset -le '@l = (1,2,3,4,5); for (@{powerset(@l)}) { print "@$_" }'

# Convert an IP address to unsigned integer
perl -le '$i=3; $u += ($_<<8*$i--) for "127.0.0.1" =~ /(\d+)/g; print $u'
perl -le '$ip="127.0.0.1"; $ip =~ s/(\d+)\.?/sprintf("%02x", $1)/ge; print hex($ip)'
perl -le 'print unpack("N", 127.0.0.1)'
perl -MSocket -le 'print unpack("N", inet_aton("127.0.0.1"))'

# Convert an unsigned integer to an IP address
perl -MSocket -le 'print inet_ntoa(pack("N", 2130706433))'
perl -le '$ip = 2130706433; print join ".", map { (($ip>>8*($_))&0xFF) } reverse 0..3'
perl -le '$ip = 2130706433; $, = "."; print map { (($ip>>8*($_))&0xFF) } reverse 0..3'

STRING CREATION AND ARRAY CREATION
----------------------------------

# Generate and print the alphabet
perl -le 'print a..z'
perl -le 'print ("a".."z")'
perl -le '$, = ","; print ("a".."z")'
perl -le 'print join ",", ("a".."z")'

# Generate and print all the strings from "a" to "zz"
perl -le 'print ("a".."zz")'
perl -le 'print "aa".."zz"'

# Create a hex lookup table
@hex = (0..9, "a".."f")

# Convert a decimal number to hex using @hex lookup table
perl -le '$num = 255; @hex = (0..9, "a".."f"); while ($num) { $s = $hex[($num%16)&15].$s; $num = int $num/16 } print $s'
perl -le '$hex = sprintf("%x", 255); print $hex'
perl -le '$num = "ff"; print hex $num'

# Generate a random 8 character password
perl -le 'print map { ("a".."z")[rand 26] } 1..8'
perl -le 'print map { ("a".."z", 0..9)[rand 36] } 1..8'

# Create a string of specific length
perl -le 'print "a"x50'

# Create a repeated list of elements
perl -le '@list = (1,2)x20; print "@list"'

# Create an array from a string
@months = split ' ', "Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec"
@months = qw/Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec/

# Create a string from an array
@stuff = ("hello", 0..9, "world"); $string = join '-', @stuff

# Find the numeric values for characters in the string
perl -le 'print join ", ", map { ord } split //, "hello world"'

# Convert a list of numeric ASCII values into a string
perl -le '@ascii = (99, 111, 100, 105, 110, 103); print pack("C*", @ascii)'
perl -le '@ascii = (99, 111, 100, 105, 110, 103); print map { chr } @ascii'

# Generate an array with odd numbers from 1 to 100
perl -le '@odd = grep {$_ % 2 == 1} 1..100; print "@odd"'
perl -le '@odd = grep { $_ & 1 } 1..100; print "@odd"'

# Generate an array with even numbers from 1 to 100
perl -le '@even = grep {$_ % 2 == 0} 1..100; print "@even"'

# Find the length of the string
perl -le 'print length "one-liners are great"'

# Find the number of elements in an array
perl -le '@array = ("a".."z"); print scalar @array'
perl -le '@array = ("a".."z"); print $#array + 1'

TEXT CONVERSION AND SUBSTITUTION
--------------------------------

# ROT13 a string
'y/A-Za-z/N-ZA-Mn-za-m/'

# ROT 13 a file
perl -lpe 'y/A-Za-z/N-ZA-Mn-za-m/' file

# Base64 encode a string
perl -MMIME::Base64 -e 'print encode_base64("string")'
perl -MMIME::Base64 -0777 -ne 'print encode_base64($_)' file

# Base64 decode a string
perl -MMIME::Base64 -le 'print decode_base64("base64string")'
perl -MMIME::Base64 -ne 'print decode_base64($_)' file

# URL-escape a string
perl -MURI::Escape -le 'print uri_escape($string)'

# URL-unescape a string
perl -MURI::Escape -le 'print uri_unescape($string)'

# HTML-encode a string
perl -MHTML::Entities -le 'print encode_entities($string)'

# HTML-decode a string
perl -MHTML::Entities -le 'print decode_entities($string)'

# Convert all text to uppercase
perl -nle 'print uc'
perl -ple '$_=uc'
perl -nle 'print "\U$_"'

# Convert all text to lowercase
perl -nle 'print lc'
perl -ple '$_=lc'
perl -nle 'print "\L$_"'

# Uppercase only the first word of each line
perl -nle 'print ucfirst lc'
perl -nle 'print "\u\L$_"'

# Invert the letter case
perl -ple 'y/A-Za-z/a-zA-Z/'

# Camel case each line
perl -ple 's/(\w+)/\u$1/g'
perl -ple 's/(?<!['])(\w+)/\u\1/g'

# Strip leading whitespace (spaces, tabs) from the beginning of each line
perl -ple 's/^[ \t]+//'
perl -ple 's/^\s+//'

# Strip trailing whitespace (space, tabs) from the end of each line
perl -ple 's/[ \t]+$//'

# Strip whitespace from the beginning and end of each line
perl -ple 's/^[ \t]+|[ \t]+$//g'

# Convert UNIX newlines to DOS/Windows newlines
perl -pe 's|\n|\r\n|'

# Convert DOS/Windows newlines to UNIX newlines
perl -pe 's|\r\n|\n|'

# Convert UNIX newlines to Mac newlines
perl -pe 's|\n|\r|'

# Substitute (find and replace) "foo" with "bar" on each line
perl -pe 's/foo/bar/'

# Substitute (find and replace) all "foo"s with "bar" on each line
perl -pe 's/foo/bar/g'

# Substitute (find and replace) "foo" with "bar" on lines that match "baz"
perl -pe '/baz/ && s/foo/bar/'

# Binary patch a file (find and replace a given array of bytes as hex numbers)
perl -pi -e 's/\x89\xD8\x48\x8B/\x90\x90\x48\x8B/g' file

SELECTIVE PRINTING AND DELETING OF CERTAIN LINES
------------------------------------------------

# Print the first line of a file (emulate head -1)
perl -ne 'print; exit'

# Print the first 10 lines of a file (emulate head -10)
perl -ne 'print if $. <= 10'
perl -ne '$. <= 10 && print'
perl -ne 'print if 1..10'

# Print the last line of a file (emulate tail -1)
perl -ne '$last = $_; END { print $last }'
perl -ne 'print if eof'

# Print the last 10 lines of a file (emulate tail -10)
perl -ne 'push @a, $_; @a = @a[@a-10..$#a]; END { print @a }'

# Print only lines that match a regular expression
perl -ne '/regex/ && print'

# Print only lines that do not match a regular expression
perl -ne '!/regex/ && print'

# Print the line before a line that matches a regular expression
perl -ne '/regex/ && $last && print $last; $last = $_'

# Print the line after a line that matches a regular expression
perl -ne 'if ($p) { print; $p = 0 } $p++ if /regex/'

# Print lines that match regex AAA and regex BBB in any order
perl -ne '/AAA/ && /BBB/ && print'

# Print lines that don't match match regexes AAA and BBB
perl -ne '!/AAA/ && !/BBB/ && print'

# Print lines that match regex AAA followed by regex BBB followed by CCC
perl -ne '/AAA.*BBB.*CCC/ && print'

# Print lines that are 80 chars or longer
perl -ne 'print if length >= 80'

# Print lines that are less than 80 chars in length
perl -ne 'print if length < 80'

# Print only line 13
perl -ne '$. == 13 && print && exit'

# Print all lines except line 27
perl -ne '$. != 27 && print'
perl -ne 'print if $. != 27'

# Print only lines 13, 19 and 67
perl -ne 'print if $. == 13 || $. == 19 || $. == 67'
perl -ne 'print if int($.) ~~ (13, 19, 67)'

# Print all lines between two regexes (including lines that match regex)
perl -ne 'print if /regex1/../regex2/'

# Print all lines from line 17 to line 30
perl -ne 'print if $. >= 17 && $. <= 30'
perl -ne 'print if int($.) ~~ (17..30)'
perl -ne 'print if grep { $_ == $. } 17..30'

# Print the longest line
perl -ne '$l = $_ if length($_) > length($l); END { print $l }'

# Print the shortest line
perl -ne '$s = $_ if $. == 1; $s = $_ if length($_) < length($s); END { print $s }'

# Print all lines that contain a number
perl -ne 'print if /\d/'

# Find all lines that contain only a number
perl -ne 'print if /^\d+$/'

# Print all lines that contain only characters
perl -ne 'print if /^[[:alpha:]]+$/

# Print every second line
perl -ne 'print if $. % 2'

# Print every second line, starting the second line
perl -ne 'print if $. % 2 == 0'

# Print all lines that repeat
perl -ne 'print if ++$a{$_} == 2'

# Print all unique lines
perl -ne 'print unless $a{$_}++'

# Print the first field (word) of every line (emulate cut -f 1 -d ' ')
perl -alne 'print $F[0]'

HANDY REGULAR EXPRESSIONS
-------------------------

# Match something that looks like an IP address
/^\d{1,3}\.\d{1,3}\.\d{1,3}\.\d{1,3}$/
/^(\d{1,3}\.){3}\d{1,3}$/

# Test if a number is in range 0-255
/^([0-9]|[0-9][0-9]|1[0-9][0-9]|2[0-4][0-9]|25[0-5])$/

# Match an IP address
my $ip_part = qr|([0-9]|[0-9][0-9]|1[0-9][0-9]|2[0-4][0-9]|25[0-5])|;
if ($ip =~ /^($ip_part\.){3}$ip_part$/) {
say "valid ip";
}

# Check if the string looks like an email address
/\S+@\S+\.\S+/

# Check if the string is a decimal number
/^\d+$/
/^[+-]?\d+$/
/^[+-]?\d+\.?\d*$/

# Check if the string is a hexadecimal number
/^0x[0-9a-f]+$/i

# Check if the string is an octal number
/^0[0-7]+$/

# Check if the string is binary
/^[01]+$/

# Check if a word appears twice in the string
/(word).*\1/

# Increase all numbers by one in the string
$str =~ s/(\d+)/$1+1/ge

# Extract HTTP User-Agent string from the HTTP headers
/^User-Agent: (.+)$/

# Match printable ASCII characters
/[ -~]/

# Match unprintable ASCII characters
/[^ -~]/

# Match text between two HTML tags
m|<strong>([^<]*)</strong>|
m|<strong>(.*?)</strong>|

# Replace all <b> tags with <strong>
$html =~ s|<(/)?b>|<$1strong>|g

# Extract all matches from a regular expression
my @matches = $text =~ /regex/g;

PERL TRICKS
-----------

# Print the version of a Perl module
perl -MModule -le 'print $Module::VERSION'
perl -MLWP::UserAgent -le 'print $LWP::UserAgent::VERSION'

• -e Makes the line of code be executed instead of a script
• -n Forces your line to be called in a loop. Allows you to take lines from the diamond operator (or stdin)
• -p Forces your line to be called in a loop. Prints $_ at the end

• This counts the number of quotation marks in each line and prints it

  perl -ne '$cnt = tr/"//;print "$cnt\n"' inputFileName.txt

• Adds string to each line, followed by tab

  perl -pe 's/(.*)/string\t$1/' inFile > outFile

• Append a new line to each line

  perl -pe 's//\n/' all.sent.classOnly > all.sent.classOnly.sep

• Replace all occurrences of pattern1 (e.g. [0-9]) with pattern2

  perl -p -i.bak -w -e 's/pattern1/pattern2/g' inputFile

• Go through file and only print words that do not have any uppercase letters.

  perl -ne 'print unless m/[A-Z]/' allWords.txt > allWordsOnlyLowercase.txt

• Go through file, split line at each space and print words one per line.

  perl -ne 'print join("\n", split(/ /,$_));print("\n")' someText.txt > wordsPerLine.txt

• or in other words, delete every character that is not a letter, white space or line end (replace with nothing)

  perl -pne 's/[^a-zA-Z\s]*//g' text_withSpecial.txt > text_lettersOnly.txt

• perl -pne 'tr/[A-Z]/[a-z]/' textWithUpperCase.txt > textwithoutuppercase.txt;

• Print only the second column of the data when using tabular as a separator

  perl -ne '@F = split("\t", $_); print "$F[1]";' columnFileWithTabs.txt > justSecondColumn.txt

• One-Liner: Sort lines by their length

  perl -e 'print sort {length $a <=> length $b} <>' textFile

• One-Liner: Print second column, unless it contains a number

  perl">perl -lane 'print $F[1] unless $F[1] =~ m/[0-9]/' wordCounts.txt

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Address of the bookmark: https://github.com/reubwn/hgt

http://genome.cshlp.org/content/early/2012/01/12/gr.131383.111

Address of the bookmark: http://gage.cbcb.umd.edu/index.html

We first operate a rapid inspection of the different BAM files using samtools flagstat. Illumina provided chr21 read mapping obtained with their GA IIx deep sequencing platform <ftp://webdata:webdata@ussd-ftp.illumina.com/Data/SequencingRuns/NA18507_GAIIx_100_chr21.bam>, aligned to the b36/hg18 reference genome)

Address of the bookmark: https://wiki.bits.vib.be/index.php/NGS_Exercise.6#compare_aln_.26_mem_results_with_vcf-compare

# plumber.R

#* Echo back the input
#* @param msg The message to echo
#* @get /echo
function(msg=""){
  list(msg = paste0("The message is: '", msg, "'"))
}

#* Plot a histogram
#* @png
#* @get /plot
function(){
  rand <- rnorm(100)
  hist(rand)
}

#* Return the sum of two numbers
#* @param a The first number to add
#* @param b The second number to add
#* @post /sum
function(a, b){
  as.numeric(a) + as.numeric(b)
}

Address of the bookmark: https://www.rplumber.io/