Lecture 2' Perl

1
Lecture 2. Perl
2
Perl

• Practical Extraction Report Language

3
What is Perl ?

• Created by Larry Wall
• Trying to create news-net like hierarchy of files
  - awk could not handle it
• Decided to create a general purpose tool
• Released Dec 1987.

4
Perl growth

• Grew rapidly in features
• Grew in portability
• gt 1,000 pages of documentation
• 600 page reference book
• Newsgroup with 200,000 subscribers

5
What is perl?
What is the sound of perl? Is it not the sound
of a wall that people have stopped banging their
heads against? -- Larry Wall.
6
What is Perl ? The language that saved the human
genome project!!

• The human genome needs 3 Gb space, just to store!
• Huge amount of sequences that need to be
  assembled!
• 1-10 terabytes information altogether!!!
• Reading http//www.stanford.edu/class/gene211/ha
  ndouts/How_Perl_HGP.html

7
Perl Pros and Cons

• Uses
• Shell scripts
• Good at
• Text processing
• Small/Medium sized projects
• Quick and dirty solutions
• Portability (to a certain degree)
• Very useful and powerful regular expressions and
  string manipulations.

8
Perl Pros and Cons

• Bad at
• Efficient large scale computation
• Neat code!

9
Basic concepts

• Perl interpreted language
• Perl program is a text file. e.g. script.pl
• Execute perl script.pl

inputs
Text editor
Perl interpreter parses the file, executes the
commands
Perl script
outputs
10
perl program

• File must indicate that it is a perl program
  not a shell program
• !/usr/bin/perl - as first line of the file

11
perl syntax

• Free format language
• Whitespace space, tab, newlines, returns.
• sign to end of line comment

12
Simple perl program

• !/usr/bin/perl -w
• print try out perl \n
• Line 1 - Indicates a perl program
• Line 1 is special - looks for optional arguments
  - like -w
• -w warning- always use it

13
Running the sample program

• Create a text file with the two lines
• Save the file eg. test.pl
• Then
• perl test.pl
• The program will be executed

14
Perl Data Types

• 3 types
• Scalar
• A single number, string or reference.
• name jelly number 2
• List or (array) of scalars
• A collection of scalar data types.
• _at_name ( john, mike, tom)
• Hash (of scalars) associative arrays
• Pairs of scalars, accessed by keys.
• hash ( color gt red,
• size gt 5 )

15
Operation of data types

• Scalar operation
• numbers same as the other language
• a 2
• , -, , /
• a b exponential. (ab)
• a b remainder of a / b

16
Operation of data types

• Scalar operation
• strings
• concatenate a b.c
• substitution a s/T/U/g
• reverse string reverse(string)
• translation str tr/ACGT/UGCA/

17
Example program

• !/usr/bin/perl w
• print Please enter your name
• name ltSTDINgt
• chomp (name)
• print you are name! \n

18
Comparison operators
19
List/Array and access elements

• Array variable names start with _at_
• _at_words (try,to,ha)
• _at_wordsqw(try to ha)
• words0 is try
• words1 is to
• i 2
• What is wordsi?

20
Array element access several functions

• foreach, pop,push, shift,unshift.
• foreach access each element in an array in order
• pop push operation on the end of an array
• shift unshift operation at the beginning of an
  array.
• _at_array (1..10)
• foreach element (_at_array)
• print element,\n
• push (_at_array, 11)
• num pop (_at_array)
• num shift (_at_array)
• num unshift (_at_array, 0..5)

21
Perl Hashes

22
Hash data type

• Associative arrays.
• Each entry is a key-value pair.
• E.g a hash stores genes their locations on the
  chromosome
• geneid_location (AF0001 gt 1200, AF0129 gt
  12450)
• id_name student_id ? student_name

23
Hash properties

• Elements are stored in perls internal order, not
  the one when you assign hash.
• Keys must be unique!!
• Values can have duplicates.

24
New elements

• stuffaaa bbb
• Creates key aaa with the value bbb
• stuff234.5 456.7
• Creates key 234.5 with the value 456.7
• print stuffaaa
• Prints bbb
• stuff234.5 3 makes it 459.7

25
Assigning values

• _at_ray_list stuff
• _at_ray_list gets (aaa,bbb,234.6,456.7)
• copy original - Copy from original to copy

26
Hash element access

• To access an element, use hashkey
• e.g.
• geneid_location (AF0001 gt 1200, AF0129 gt
  12450)
• where geneid_locationAF0001
• geneid_locationAF3224 21000
• Hash elements are stored in perls own order.

27
Hash element access

• keys and values functions
• keys results in a list of all current keys in
  the hash
• values results in a list of all the values in
  the hash
• geneid_location (AF0001 gt 1200, AF0129
  gt 12450, AF3224 gt 21000)
• _at_geneid keys geneid_location
• _at_location values geneid_location

28
Hash element access

• each function iterate over the entire hash.
• While ((key,value) each geneid_location)
• print key,gt, value, \n

29
Hash operation

• delete function remove the key-value pair
• delete geneid_locationAF0001
• exists function check whether certain key
  exists.
• if (exists geneid_locationAF0001)
• print gene AF0001 exists\n

30
Control statements

• If else
• if (name eq Ray)
• print Hello Ray\n
• else
• print what is your name?\n
• If elsif elsif else

31
Boolean values

• False True
• Undef all other numeric values
• 0
• empty string all other strings
• 0

32
Control statements

• unless
• e.g.
• unless (change gt 0)
• print change can not be negative value!\n
• while zero or more times loop.
• for e.g for (j0jlt5j) statements

33
subroutines
!/usr/bin/perl w dna1 ggg long1
addACGT(dna1) print long1\n sub addACGT
my (dna) _at__ dna ACGT return
dna
34
subroutines

• my restrict the scope of the variable to the
  body of the subroutine.
• The values that are passed to subroutine are
  stored in _at__
• dna1 ? subroutine _at__

35
subroutines
e.g. call addon (dna1, dna2, dna3) sub addon
my (s1,s2,s3) _at__
36
Subroutine and references

• Usually pass by value to subroutine.
• Pass by reference
• Reference holds the address of the variable it
  points to.

37
references

• a_ref \a
• array_ref \_at_array
• hash_ref \hash
• To use the variable referenced, we need to
  dereference the reference.
• Append , _at_, in front of the reference.
• a_ref, _at_array_ref, hash_ref

38
example

• _at_i 1..10
• _at_j (a,b,z)
• reference_sub(\_at_i,\_at_j)
• sub reference_sub
• my (i,j) _at__
• print first _at_i\n
• push (_at_j, s)
• print _at_j

39
PERLContinuation

40
Regular Expressions

• Regular expression is a pattern, describe a
  string, or a whole family of strings via
  wildcards.
• Matching a regular expression against a string
  either succeeds or fails.

41
Simple use of regular expressions

• Grep command - One of Unixs most useful tools.
• Used for searching with regular expressions.

42
Using grep

• Find all lines in a file containing the string
  abc.
• Grep abc somefile
• abc is the regular expression tested against each
  input line.
• Matching lines sent to standard output.

43
Perl regular expression

• Regular expressions in perl is enclosed in
  slashes, / /.
• Use match operator

44
Regular expressions

• if(name /Bell/)
• print ("string matches")

45
Ignore case option

• Small i after closing slash Ignore case
• / /i
• To reject Belle - add word boundary \b
• \b - Insures no other letter follows pattern.

46
Revised string

• /Bell\b/i
• Bell at beginning of string
• No letter or digit following
• OK in either upper or lower case
• Matches bell, Bell, etc. but not belle

47
Regular expression

• Reg. exp build patterns based on 3 fundamental
  ideas
• Repetition
• Alternation
• concatenation

48
Regular expression

• /fossil/ match fossil and fossiliferous
• To increase the power of regex, use
  metacharacters
• Repetition , , ?,
• one or more times
• zero or more times
• ? zero or one time
• 2, 4 occur between 2 and 4 times

49
Regular expression

• metacharacters
• Alternation
• Alternatives are separated by (or)
• dna ATGCGA
• dna s/AGCT/2/g
• print dna, \n

50
Regular expression

• metacharacters
• parenthesis () grouping
• Use to group characters.
• /a(bat)/ match abat, abatbat, abatc, etc.
• Character class
• abc match any of the chars in the square
  bracket.

51
Regular expression
52
Regular expression

• Pattern anchors
• matches the beginning of the string
• matches the end
• /where/ matches any string starts with where
• /world/ matches anything ends with world

53
Substitute operator

• Find a regular expression replace with a string
• s/form1/form2/ substitute form 1 with new form.
• dna ATCttG
• dna s/T/U/ig substitute all Ts with Us
• i and g are pattern modifiers.
• i ignore cases
• g globally

54
Using files for input/output

• Consider a file protein.seq which contains the
  following data
• MNIDDKL
• SVLQ
• GLQVLL
• Problem read in the file.

55
Using files for input/output

• !/usr/bin/perl w
• file protein.seq
• open the file and associate a filehandle.
• open (IN, file)
• read the first line from the file into a
  variable
• protein ltINgt
• print protein, \n
• read the second line
• protein ltINgt
• print protein, \n
• close IN

56
Using files for input/output

• Several standard predefined file handles
• STDIN
• STDOUT
• STDERR
• e.g.
• protein ltSTDINgt
• chomp protein
• print protein, \n
• Perl will wait for the user to command line
  input.

57
Writing output to a file

• file output
• open (OUT, gtfile)
• print OUT protein\n
• print to console
• print protein\n
• the same as above
• print STDOUT protein\n

58
Command line arguments

• _at_ARGV hold command line arguments.
• e.g. test.pl.
• !/usr/bin/perl w
• unless (_at_ARGV)
• print usage test.pl argument\n
• exit
• input ARGV0
• print input\n
• perl test.pl 5

59
miscellaneous about perl

• use strict
• Requires all variables be declared by my before
  using them.
• my variable 3
• A good habit always use strict to start your
  program.
• This will prevent mistakes such as typos

60
Perl process management

• To launch a process from a perl script, use
  system
• e.g.
• system date
• system ls
• Commands will be executed by the unix shell.
• Perl will wait for the process to terminate
  before it continues.
• The new process is a child of the shell.

61
Capture the system output

• Use command
• _at_files ls /home/zhang
• _at_files have all the output of ls command.

62
Context dependent scalar or list?

• perl operations behave differently depending on
  the context.
• e.g.
• _at_array 1..10
• b _at_array b is now ?

63
An example perl script

• count Gs in command-line DNA
• !/usr/bin/perl w
• use strict
• my (usage) 0 DNA\n\n
• unless (_at_ARGV)
• print usage
• exit
• my (dna) ARGV0
• my (num_of_g) countG(dna)
• print num_of_g\n
• exit
• sub countG
• my (dna) _at__
• my (count) 0
• count while (dna /g/ig)

64
(No Transcript)
65
Here are the arrays of parts of sentences my
_at_nouns ( 'Dad', 'TV', 'Mom', 'Groucho', 'Rebecca
', 'Harpo', 'Robin Hood', 'Joe and Moe', )
66
my _at_verbs ( 'ran to', 'giggled with', 'put hot
sauce into the orange juice of', 'exploded', 'diss
olved', 'sang stupid songs with', 'jumped
with', )
67
my _at_prepositions ( 'at the store', 'over the
rainbow', 'just for the fun of it', 'at the
beach', 'before dinner', 'in New York City', 'in
a dream', 'around the world', )
68
Seed the random number generator. time
combines the current time with the current
process id in a somewhat weak attempt to come
up with a random seed. srand(time) This
do-until loop composes six-sentence "stories".
until the user types "quit". do story
''
69
for (count 0 count lt 6 count)
sentence nounsint(rand(scalar _at_nouns))
. " " .
verbsint(rand(scalar _at_verbs))
. " " . nounsint(rand(sca
lar _at_nouns)) . " "
. prepositionsint(rand(scalar
_at_prepositions)) . '. '
story . sentence
70
print "\n",story,"\n" Get user input.
print "\nType \"quit\" to quit, or press Enter
to continue " input ltSTDINgt Exit
loop at user's request until(input
/\sq/i) exit
71
Perl resource

• Online perl series
• learning perl.
• perl cookbook.
• www.perl.com
• The Perl Bible
• Perl In a Nutshell OReilly