# 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'

Address of the bookmark: https://github.com/SAMtoBAM/MUMandCo

How does SEX-DETector work?

SEX-DETector does not require prior sequencing of a reference genome: the same sequencing data can be used for the assembly and for the mapping of the reads. A full documentation on the pipeline can be found here.

• we recommend Trinity for the assembly.
• Trinity components should be merged with cap3. Our code to perform the merging is available here.
• We recommend BWA for mapping of the reads.
• When the mapping has been perfomed, the individuals need to be genotyped; SEX-DETector takes files produced by Reads2snp (which is available for download on the PopPhyl website) as input.

Address of the bookmark: http://lbbe.univ-lyon1.fr/-SEX-DETector-.html?lang=eg

Mulan (http://mulan.dcode.org/), a novel method and a network server for comparing multiple draft and finished-quality sequences to identify functional elements conserved over evolutionary time. Mulan brings together several novel algorithms: the TBA multi-aligner program for rapid identification of local sequence conservation, and the multiTF program for detecting evolutionarily conserved transcription factor binding sites in multiple alignments. In addition, Mulan supports two-way communication with the GALA database; alignments of multiple species dynamically generated in GALA can be viewed in Mulan, and conserved transcription factor binding sites identified with Mulan/multiTF can be integrated and overlaid with extensive genome annotation data using GALA.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC540288/

Finally, I find the underlying R code in a file created by GrapheR. For more details read also the package vignette, which is available in English, French and German!

More at http://pythonhosted.org/pybedtools/

A powerful toolset for genome arithmetic.http://code.google.com/p/bedtools/

Please visit our site at www.arraygen.com

Essential qualifications: First class M. Sc. in any branch of life sciences and qualified CSIR-UGC NET/GATE Examination.

Desirable qualifications: Practical experience in biochemical and biophysical studies of proteins

Emoluments: as per DBT norms

The project is tenable for two years, initially for one year.

Age: Below 28 years (relaxable in the case of SC/ST/OBC/women candidates)

Candidates are requested to bring two sets of complete applications on plain paper furnishing bio-data and copies of attested certificates along with originals (for verification) on the date of interview.

No TA/DA is admissible for candidates appearing at the interview.

Dr. Rajat Banerjee
Assistant Professor
Department of Biotechnology and
Dr. B. C. Guha Centre for Genetic Engineering and Biotechnology
University College of Science
35, Ballygunge Circular Road
Kolkata 700019

Advertisement: www.caluniv.ac.in/news/jrf_biotech_2.pdf

Walk-in-Interview will be held on 04th March 2015 at 11.30 A.M. in the Bio- Informatics Centre of Bose Institute, P-1/12, C.I.T. Scheme VII-M, Kolkata- 700054 for two (02) positions of Research Associate/ Extended Senior Research Fellow in the DBT sponsored following two projects running under the CoE- Bioinformatics under the guidance of Prof. Pinakpani Chakrabarti, Bioinformatics Centre.

Position : RA/SRF
Project title : 1. "Centre of Excellence (CoE) in Bioinformatics at Bose Institute”,2. Project entitled “Setting up of National Facility on Interactive Graphysics Computer System (IGCS) for Biomolecular Modeling, Molecular Dynamics & Structures”

Desired Profile : Ph.D degree in Biological or Chemical Sciences with in-depth understanding of protein structure and dynamics for R.A. position.Those who have submitted thesis can be considered for Extended SRF position
Preferred : Knowledge of computer programming and bioinformatics softwares.
Stipend : For R.A- Rs. 22,000/- p.m., plus admissible H.R.A. and Medical benefit. For Extended SRF - Rs. 20,000/- p.m., plus admissible H.R.A.and Medical benefit.
Age : For R.A- Below 35 years; For Extended SRF - Below 33 years
Interested and eligible candidates should appear before the Selection Committee with atyped application addressed to the Sr.Prof. & In-Charge, Registrar's Office, Bose Institute, P- 1/12, CIT Scheme VII-M, Kankurgachi, Kolkata-700054 along with Bio-data giving details of qualification i.e. examination passed, year, division, percentage of marks from Secondary onwards with attested copies of Certificates, Mark-Sheet and testimonials. The candidates should also bring the original mark-sheets, certificates etc. at the time of Interview.

Walk in Interview : 04.03.15

More at http://www.boseinst.ernet.in/ADVT/14/p_34.pdf