BNFO 135

1
Lecture 2

• BNFO 135
• Usman Roshan

2
Perl variables

• Scalar
• Number
• String
• Examples
• myname Roshan
• year 2006

3
Number operators
4
Strings

• Perl supports very powerful operations on
  strings. Basic operators below.

5
Arrays

• Array variables begin with _at_.
• Example
• _at_myarray(1,2,3,4,5)
• _at_s(dna, rna, protein)
• print _at_s outputs dnarnaprotein

6
Array operations
7
Hashes

• Hashes are like arrays, except that they are
  indexed by user defined keys instead of
  non-negative integers.
• Hashes begin with
• Examples
• h(red, 1, blue, 2, green, 3)
• h(first, usman, last, name)

8
Perl online references

• http//www.rexswain.com/perl5.html
• http//www.perl.com/pub/q/documentation
• http//www-cgi.cs.cmu.edu/cgi-bin/perl-man
• http//www.squirrel.nl/pub/perlref-5.004.1.pdf
• http//perldoc.perl.org/index-language.html

9
Input and Output

• printf C-like formatted output, very powerful
• print unformatted output
• Example
• printf My name is s\n, name
• printf Today is s d d\n, month, day, year

10
File I/O

• open(IN, in.txt)
• lineltINgt
• print line
• close IN
• open(OUT, gtout.txt)
• print OUT line1\n
• close OUT

11
File I/O

• open(OUT, gtgtout.txt)
• print OUT line2\n
• close OUT
• open(IN, in.txt)
• _at_linesltINgt reads all lines into array
• print _at_lines
• close IN
• inputltSTDINgt read from standard input

12
Control structures---if else block

• if (c)
• s1 s2 ...
• if (c)
• s1 s2...
• else
• s1 s2...

• if (c1)
• s1 s2 ...
• elsif (c2)
• ...
• elsif (c3)
• ....
• else
• ...

13
Control structures---if else block

• This is program to compute max of two
• Numbers.
• max0
• if(x gt y) max x
• else max y

14
Control structures---for loop

• for(init_exp test_exp iterate_exp)
• s1 s2
• foreach i (_at_some_list) s1 s2 ...
• Examples
• for (i0 i lt _at_arr i)
• print arri
• foreach e (_at_arr)
• print e

15
Control structures---while loop

• while (condition) s1 s2...
• do s1 s2 ... while condition
• while (condition) s1if(c)last s2...
• last means exit the loop
• while (condition) s1if(c)next s2...
• next means go to next iteration

16

• Write a program to prompt the user for a Yes or
  No response. Read in the user response using the
  STDIN file handle and print OK is the user
  enters Yes, I hear you if the user enters
  No, and Make up your mind! if the user enters
  something other than Yes or No.
• Create a script called foods.pl that asks the
  user for their favorite foods. Ask the user to
  enter at least 5 foods, each separated by a space
  (or some other delimiter). Store their answer in
  a scalar. Split the scalar into an array. Once
  the array is created, have the script do the
  following
• Print the array
• Print the number of elements in the array
• Create an array slice from three elements
  of the array and print the new array
• Write a program to open a file containing SSNs
  and read in the first five records into an array.

17

• Write a program called count.pl that reads in a
  set of strings from a file called string.txt and
  prints the number of As, Bs, Cs, and Ds. For
  example, if the file looks like
• AABCAA
• CDAAD
• CCC
• then your program should output
• A 6
• B 1
• C 5
• D 2

18
Subroutines

• sub ltsubroutine_namegt
• parameters are placed in _at__
• ltcodegt
• .
• .
• return

19
Scope

• You can create local variables using my.
• Otherwise all variables are assumed global, i.e.
  they can be accessed and modified by any part of
  the code.
• Local variables are only accessible in the scope
  of the code.

20
Pass by value and pass by reference

• All variables are passed by value to subroutines.
  This means the original variable lying outside
  the subroutine scope does not get changed.
• You can pass arrays by reference using \. This is
  the same as passing the memory location of the
  array.

21
Splitting and joining strings

• split splits a string by regular expression and
  returns array
• _at_s split(/,/)
• _at_s split(/\s/)
• join joins elements of array and returns a
  string (opposite of split)
• seqjoin(, _at_pieces)
• seqjoin(X, _at_pieces)

22
Searching and substitution

• x /y/ ---- true if expression y found in
  x
• x /ATG/ --- true if open reading frame ATG
  found in x
• x ! /GC/ --- true if GC not found in x
• x s/T/U/g --- replace all Ts with Us
• x s/g/G/g --- convert all lower case
  g to upper case G

23
DNA regular expressions
Taken from Jagotas Perl for Bioinformatics