getting started with perl (and excel)
DESCRIPTION
Getting Started with Perl (and Excel). Biophysics 101 September 17, 2003 Griffin Weber (With material from Jon Radoff and Ivan Ovcharenko). What is a computer?. Artificial brains? Smarter than you? Too complicated to understand?. What is a computer?. A machine with lots of buttons - PowerPoint PPT PresentationTRANSCRIPT
Getting Started with Perl
(and Excel)
Biophysics 101
September 17, 2003
Griffin Weber
(With material from Jon Radoff and Ivan Ovcharenko)
What is a computer?
• Artificial brains?
• Smarter than
you?
• Too complicated
to understand?
What is a computer?
• A machine with lots of buttons
• The “3 minute popcorn” program:
TIME 300
STARTcommands
parameter
What is a computer?
01100101 10101101
Input Output
0 = off1 = on
What is Perl?
• Perl is a computer language• Easier to use than binary code
01100101print 2+3;
Perl
Interpreter
Where do I get Perl?
Course web site for download links and instructions:http://www.courses.fas.harvard.edu/~bphys101/links/
index.html
Windows: ActivePerl
MacOS: MacPerl
Unix/Linux (FAS): Already Installed
How do you use Perl?
• Create a new text file• Type all the commands• Save it as a *.pl file (hello.pl)• Tell the computer to run your file
perl hello.pl
What does Perl look like?
#!/usr/local/bin/perl
print “Hello everyone\n”;
Mandatory first line !
Draw something to the screen
Printing Output to the Screen
print “Hello \n”;
print command:
" " - place output in quotes
\n - end-of-line character
(like pressing ‘Enter’)
; - ends every command
Variables
2+2 = ? $a = 2;
$b = 2;
$c = $a + $b;
$ - indicates a variable
;
= - assigns a value to a variable
- don’t forget
a - the variable name
Perl Calculator
$c = 4 - 2;
$c = 2 * 2;
$c = 2 / 2;
$c = 2 ** 4; - power : 2^4 <-> 24
=16$c = 1.35 * 2 – log(3) / (0.12 + 1);
- subtract
- multiply
- divide
natural log
Perl Calculator : Output
print " 2 + 2 = " . (2+2) . "\n";
$c = 2 + 2;
print " 2 + 2 = $c \n";
print the value of $c
2 + 2 = 4
or… strings
expressionconcatenate.output
Datatypes
# DEFINING NUMBERS
$x = 4;
$x = 1.25;
$x = 2.345e-56;
# DEFINING STRINGS
$x = “ACTGGTA”;
$y = “Hello everyone \n”;
2.345 * 10-56
2.345*10**-56
Perl Examples:# - comment
line (Perl ignores)
Loops and Cycles : FOR Statement
# Output all the numbers from 1 to 100
for ($n=1; $n<=100; $n+=1) {
print “$n \n”;
}
1. Initialization
for ( $n=1 ; $n<=100 ; $n+=1 ) { … }
4. Increment ($n = $n + 1)
2. Termination (stop if this is not true)
3. Body (or block) of the loop - commands inside curly brackets
FOR Loop Example
Output - Triangle of A’s:
for ($line=1; $line<=3; $line+=1) {
# output $line ‘A’ symbols
for ($n=1; $n<=$line; $n+=1) {
print “A”;
}
# end the line
print “\n”;
}
AAAAAA
Source code:
Indent = TA
Conditional Statements$x = -1;
# check whether $x is positive or not
if ($x > 0) {
print “x = $x is positive\n”;
}
1. If this is true, ...
if ( some_expression ) { … }
2. ... then do this - commands inside curly brackets
Expressions
$x = 1;
$y = 2;
if ($x < $y) { }
if ($x > $y) { }
if ($x <= $y) { }
if ($x >= $y) { }
if ($x == $y) { }
if ($x != $y) { }
With numbers:
Less than
Greater than
Less than or equal
Greater than or equal
Equal
Not equal
$a = “DNA”;
$b = “RNA”;
if ($a lt $b) { }
if ($a gt $b) { }
if ($a le $b) { }
if ($a ge $b) { }
if ($a eq $b) { }
if ($a ne $b) { }
With strings:
Conditional Statements
Output:
$x = -1;
# check whether $x is positive or not
if ($x > 0) {
print “x = $x is positive\n”;
}
if ($x < 0) {
print “x = $x is negative\n”;
}
if ($x == 0) {
print “x is zero\n”;
}
x = -1 is negative
Source code:
Conditional Statements
$x = -1;
# check whether $x is positive or not
if ($x > 0) {
print “x = $x is positive\n”;
} elsif ($x < 0) {
print “x = $x is negative\n”;
} else {
print “x is zero\n”;
}
The same thing:
if ( some_expression ) { … } else { … }
if this is true do this otherwise do this
Putting It Together
FOR & IF -- all the even numbers from 1 to 100:
for ($n=1; $n<=100; $n+=1) {
if (($n % 2) == 0) {
print “$n”;
}
}Note: $a % $b -- Modulus (remainder when $a is divided by $b)
7 % 2 = 1 5 % 3 = 2 12 % 4 = 0
Data Structures : Arrays
# array of 5 numbers
@a = (7,3,4,-1,0);
# array of strings
@day = (“Mon”, “Tue”, “Wed”, “Thu”, “Fri”);
@ - indicates an array (…)
- a list of values
$a[2] - an element of the array (count from 0)
Data Structures : Arrays@a = (7,3,4,-1);
# change the value of an element$a[1] = 5;
# print all the elements in the array @a
for ($i=0; $i<=$#a; $i+=1) {
print “a[$i] = $a[$i] \n”;
}
$#a - the index of the last element in the array @a
a[0] = 7
a[1] = 5
a[2] = 4
a[3] = -1
Two Dimensional Arrays
# A 2x2 array of 9 numbers
@a = ([1,2,3],[4,5,6],[7,8,9]);
([…],[…],…,[…])
- an array of arrays
# change the value of an element
$a[1][2] = -1;
print “ $a[2][0] \n”;7
Working with Files
Microsoft Word
Open
Edit
Save
Close
Perl Files
Open
Read or Write(one line at a time)
Close
Working with Files
How to open and close a file “data.txt” from a perl program? # open data.txt file for READINGopen (FILE, "<data.txt" );
File handler -This name will be used everywhere later in the program, when we will deal with this file.
<>
Direction of file data flow
- READ from a file
# close a file specified by FILE file handlerclose (FILE);
- WRITE to a file
Working with Files
Writing “Hello everyone” to the “tmp.txt” file:
#!/usr/local/bin/perl
open (FILE, “>tmp.txt”);
print FILE “Hello everyone\n”;
close (FILE);
Note: If tmp.txt already exists, it will be erased.
Working with Files
# open file data.txt for readingopen (FILE, “<data.txt”);
# read file line by line and print it out to the
screen
while ($line = <FILE>) {
print “$line”;
}
#close fileclose(FILE); while loop is analogous to the for loop.
All the body statements of it are executed until the condition in parenthesis is false.
Read the next line from the file specified by the filehandle <FILE>
Working with FilesExample. Calculating a sum of numbers in the file data.txt:
#!/usr/local/bin/perl$sum = 0;open (FILE, “<data.txt”);while ($line = <FILE>) {
chomp($line);$sum = $sum + $line;
}close(FILE);print “Sum of the numbers in data.txt file is $sum\n”;
118232
Sum of the numbers in data.txt file is 44
chomp command removes “\n” (new line) symbol from the string
More Strings
$DNA = “ACGTCG”;
# length of the string -> number of characters
inside
$seqLen = length ($DNA); # $seqLen =
6
# extracting a part of a string
$seqPart = substr ($DNA, 2, 3); # $seqPart =
“GTC”
substr ( $string, $offset, $n)
-- extracts $n characters from the string
$string, starting at the position $offset
(first position in a string is 0, not 1!)
Note: In Perl, a string is not an array of characters.
More Strings$DNA = “ACGTCG”;
# length of the string -> number of characters
inside
$seqRev = reverse ($DNA); # $seqRev =
“GCTGCA”
# substitute all ‘C’ symbols with ‘T’ symbols
$DNA =~ s/C/T/gi; # $DNA = “ATGTTG”s - substitute
(search & replace)
g – global (everywhere)
i – case insensitive
# count the number of substitutions
$numG = ($DNA =~ s/G//gi); # $numG = 2
More Strings
$str = “I like biology.”;
# replace “biology” with “computers”$str =~ s/biology/computers/; # $str = “I like computers.”
# replace ‘r’ with ‘n’, ‘e’ with ‘i’, and ‘s’ with ‘g’$str =~ tr/res/nig/; # $str = “I liki computing.”
Note: tr/// substitutes only symbols, while s/// substitutes strings
Functions (Subroutines)
$x = min(5,3);print “Smallest of 5 and 3 is: $x\n”;
# Function minsub min {
($a, $b) = @_;if ($a < $b) {
$small = $a;} else {
$small = $b;}return $small;
}
A function is a program within a program.
define the function
input parameters
return the answer
call the function
ModulesPerl does not have functions for everything, but many useful functions have already programmed by other people, and they share their libraries of functions, which are called modules
use bignum; # Work with large numbers
use CGI; # Build interactive web pages
use BioPerl; # Perform DNA sequence analysis
use GD; # Create pictures
use DBI; # Communicate with databaseshttp://cpan.org/ -- lots of Perl modules
use X; - place near the beginning of your program
tells Perl to use all the functions in module X
Bugs!
$x = 1if ($x = 1) { $x = 2; }x = 0;$a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1if ($x = 1) { $x = 2; }x = 0;$a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1;if ($x = 1) { $x = 2; }x = 0;$a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1;if ($x == 1) { $x = 2; }x = 0;$a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1;if ($x == 1) { $x = 2; }$x = 0;$a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1;if ($x == 1) { $x = 2; }$x = 0;@a = (1, 2, 3);$y = 5/$x;
Bugs!
#!/usr/local/bin/perl $x = 1;if ($x == 1) { $x = 2; }$x = 0;@a = (1, 2, 3);$y = 5/$x; # divide by 0
Excel
• What is a worksheet?
• Enter data by hand
• Import data from a file
• Use Excel built-in functions
• Perform statistical tests
• Make graphs from data