Programming and Perl for Bioinformatics Part I

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Programming and Perlfor BioinformaticsPart I
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Why Write Programs?

• Automate computer work that you do by hand - save
  time and reduce errors
• Run the same analysis on lots of similar data
  files scale-up
• Analyze data, make decisions
• sort Blast results by e-value and/or species of
  best mach
• Build a pipeline
• Create new analysis methods

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Why Perl?

• Fairly easy to learn the basics
• Many powerful functions for working with text
  search extract, modify, combine
• Can control other programs
• Free and available for all operating systems
• Most popular language in bioinformatics
• Many pre-built modules are available that do
  useful things

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Get Perl

• You can install Perl on any type of computer
• Just log in - you dont even need to type any
  command to make Perl active.
• Download and install Perl on your own computer
• www.perl.org

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Programming Concepts

• Program a text file that contains instructions
  for the computer to follow
• Programming Language a set of commands that the
  computer understands (via a command
  interpreter)
• Input data that is given to the program
• Output something that is produced by the
  program

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Programming

• Write the program (with a text editor)
• Run the program
• Look at the output
• Correct the errors (debugging)
• Repeat
• computers are VERY dumb -they do exactly what you
  tell them to do, so be careful what you ask for

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Strings

• Text is handled in Perl as a string
• This basically means that you have to put quotes
  around any piece of text that is not an actual
  Perl instruction.
• Perl has two kinds of quotes
• - single ... and double ...
• (they are different- more about this later)

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Print

• Perl uses the term print to create output
• Without a print statement, you wont know what
  your program has done
• You need to tell Perl to put a carriage return at
  the end of a printed line
• Use the \n (newline) command
• Include the quotes
• The \ character is called an escape - Perl
  uses it a lot

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A Taste of Perl print a message

• hello_world.pl Greet the entire world.
• !/usr/bin/perl -w
• greet the entire world
• x 6e9
• print Hello world!\n
• print All x of you!\n

- command interpretation header
- a comment
- variable assignment statement

- function calls (output statements)
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Variables

• Up till now, weve been telling the computer
  exactly what to print. But in order for the
  program to generate what is printed, we need to
  use variables.
• A scalar variable name starts with
• It can store either a string or a number.

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Basic Syntax and Data Types

• whitespace doesnt matter to Perl. One can write
  all statements on one line
• All Perl statements end in a semicolon just
  like C
• Comments begin with and Perl ignores
  everything after the until end of line.
• Example this is a comment
• Perl has three basic data types
• scalar
• array (list)
• associative array (hash)

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Variables

• To be useful at all, a program needs to be able
  to store information from one line to the next
• Perl stores information in variables
• A scalar variable name starts with the
  symbol, and it can store strings or numbers
• Variables are case sensitive
• Give them sensible names
• Use the sign to assign values to variables
• one_hundred 100
• my_sequence ttattagcc

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Scalars

• Scalar variables begin with followed by an
  identifier
• Example this_is_a_scalar
• An identifier is composed of upper or lower case
  letters, numbers, and underscore '_'. Identifiers
  are case sensitive (like all of Perl)
• progname first_perl
• numOfStudents 4
• ( gets) sets the content of progname to be
  the string first_perl and numOfStudents to be
  the integer 4

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Scalar Values

• Numerical Values
• integer 5, 3, 0, -307
• floating point 6.2e9, -4022.33
• NOTE all numerical values stored as
  floating-point numbers (double precision)

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A program with variables

• !/usr/bin/perl -w
• this program uses variables containing numbers
• my two 2
• my three two 1
• print \two \three two three ",
• (two three)
• print "\n"

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Do the Math

• Mathematical functions work pretty much as you
  would expect
• 47
• 64
• 43-27
• 256/12
• 2/(3-5)
• Example
• !/usr/bin/perl
• print "45\n"
• print 45 , "\n"
• print "45" , 45 , "\n"
• myNumber 88
• Note use commas to separate multiple items in a
  print statement

45 9 459
What will be the output?
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Scalar Values

• String values
• Example
• day "Monday "
• print "Happy Monday!\n"
• print "Happy day!\n"
• print 'Happy Monday!\n'
• print 'Happy day!\n'
• Double-quoted interpolates (replaces variable
  name/control character with its value)
• Single-quoted NO interpolation done (as-is)

Happy Monday!ltnewlinegt
Happy Monday!ltnewlinegt
Happy Monday!\n
Happy day!\n
What will be the output?
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String Manipulation

• Concatenation
• dna1 ACTGCGTAGC
• dna2 CTTGCTAT
• juxtapose in a string assignment or print
  statement
• new_dna dna1dna2
• Use the concatenation operator .
• new_dna dna1 . dna2
• Substring
• dna ACTGCGTAGC
• exon1 substr(dna,2,5)

TGCGT
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Substitution

• DNA transcription T ? U
• Substitution operator s///
• dna GATTACATACACTGTTCA
• rna dna
• rna s/T/U/g GAUUACAUACACUGUUCA
• is a binding operator indicating to exam the
  contents of rna for a match pattern g
  global
• Ex Start with dna gaTtACataCACTgttca
• and do the same as above. What will be the output?

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Example

• transcribe.pl
• dna "gaTtACataCACTgttca"
• rna dna
• rna s/T/U/g
• print "DNA dna\n"
• print "RNA rna\n"
• Does it do what you expect? If not, why not?
• Patterns in substitution are case-sensitive! What
  can we do?
• Convert all letters to upper/lower case (
  preferred when possible )
• If we want to retain mixed case, use
  transliteration/translation operator tr///
• rna tr/tT/uU/ replace all t by u, all T
  by U

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Case conversion

• string acCGtGcaTGc
• Upper case
• dna uc(string) ACCGTGCATGC
• or dna uc string
• or dna \Ustring \U string directive
• Lower case
• dna lc(string) accgtgcatgc
• or dna \Lstring
• Sentence case
• dna ucfirst(string) Accgtgcatgc
• or dna \u\Lstring

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Reverse Complement

• 5- A C G T C T A G C . . . . G C A T -3
• 3- T G C A G A T C G . . . . C G T A -5
• Reverse reverses a string
• string "ACGTCTAGC"
• string reverse(string) "CGATCTGCA
• Complementation use transliteration operator
• string tr/ACGT/TGCA/

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Whats Wrong?

• DNA "ACGTCTAGC"
• print "DNA\n\n"
• revcom reverse DNA
• Next substitute all bases by their
  complements,
• A-gtT, T-gtA, G-gtC, C-gtG
• revcom s/A/T/g
• revcom s/T/A/g
• revcom s/G/C/g
• revcom s/C/G/g
• Print the reverse complement DNA onto the
  screen
• print "revcom\n"

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More on String Manipulation

• String length
• length( dna )
• Index
• index STR,SUBSTR,POSITION
• index( strand, primer, 2 )

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Flow Control

• Conditional Statements
• parts of code executed depending on truth value
  of a logical statement
• truth (logical) values in Perl
• false 0, 0.0, 0e0, , undef, default
• true anything else, default 1
• (a, b) (75, 83)
• if ( a lt b )
• a b
• print Now a b!\n
• if ( a gt b ) print Yes, a gt b!\n
  Compact

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Comparison Operators
Comparison String Number
Equality eq
Inequality ne !
Greater than gt gt
Greater than or equal to ge gt
Less than lt lt
Less than or equal to return 1/null le lt
Comparison Returns -1, 0, 1 cmp ltgt
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Logical Operators
Operation Computerese English version
AND and
OR or
NOT ! not
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if/else/elsif

• allows for multiple branching/outcomes
• a rand()
• if ( a lt 0.25 )
• print A
• elsif (a lt 0.50 )
• print C
• elsif ( a lt 0.75 )
• print G
• else
• print T

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Whats a block?

• In the case of an if statement
• If the test is true, execute all the command
  lines inside the brackets. If not, then go on
  past the closing to the statements below.
• You can also do stuff in a block over and over
  again using a loop.

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Conditional Loops

• while ( statement ) commands
• repeats commands until statement is no longer
  true
• do commands while ( statement )
• same as while, except commands executed as least
  once
• NOTE the after the while statement
• Short-circuiting commands next and last
• next jumps to end, do next iteration
• last jumps out of the loop completely

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While-Loop

• Loops test a condition and repeat a block of code
  based on the result
• while loops repeat while the condition is true
• count 1
• while (count lt 10)
• print count bottles of pop\n
• count count 1
• print POP!\n
• Try this program yourself

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for and foreach loops

• Execute a code loop a specified number of times,
  or for a specified list of values
• for and foreach are identical use whichever you
  want
• Incremental loop (C style)
• for ( i0 i lt 50 i )
• x ii
• print "i squared is x.\n"
• Loop over list (foreach loop)
• foreach name ( "Billy", "Bob", "Edwina" )
• print "name is my friend.\n"

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Standard Input

• To make the program do something, we need to
  input data.
• The angle bracket operator (lt gt) tells Perl to
  expect input, by default from the keyboard.
• Usually this is assigned to a variable
• print Please type a number
• num ltSTDINgt
• print Your number is num\n

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chomp

• When data is entered from the keyboard, the
  program waits for you to type the carriage return
  key.
• But.. the string which is captured includes a
  newline (carriage return) at its end
• You can use the chomp function to remove the
  newline character
• print Enter your name
• name ltSTDINgt
• print Hello name, happy to meet you!\n
• chomp name
• print Hello name, happy to meet you!\n

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Basic Data Types

• Perl has three basic data types
• scalar
• array (list)
• associative array (hash)