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Perl has three data types

Perl has three data types. $ - Scalar: holds a single value, which can be a number or string, $EcoRI = ‘GAATTC’; @ - Array: stores multiple scalar values [0, 1, 2, etc.] % - Hash: An associative array with keys and values. End of chapter 4-beginning of chapter 5. Arrays.

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Perl has three data types

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  1. Perl has three data types • $ - Scalar: holds a single value, which can be a number or string, $EcoRI = ‘GAATTC’; • @ - Array: stores multiple scalar values [0, 1, 2, etc.] • % - Hash: An associative array with keys and values End of chapter 4-beginning of chapter 5

  2. Arrays • An array is an ordered list of data • An array variable begins with an @ • @array1 = (1, 2, 3, four); #array1 has five elements

  3. Element Access • An array element can be accessed via a numeric index • Array elements are numbered sequentially by integers beginning at zero • @array1 = (1, 2, 3); • $a = @array1[2]; #$a is 3 • $array[1] = 6; #@array1 is (1, 6, 3) • $array1[0] ++; #@array1 is (2, 6, 3)

  4. Push and Pop • Push will insert an element at the end of the array. • Pop will remove and return the last element from an array • Push(@array1, 2, 4, 6); #@array1 is (1, 3, 5, 2, 4, 6) • $last = pop(@array1); # $last is 6

  5. Shift and unshift • Shift removes and returns the first element of the array • Unshift inserts an element to the beginning of the array • Unshift (@array1, 7, 8); #@array1 is (7, 8, 1, 3, 5, 2, 4, 6) • $first = shift (@array1); #@array is (8, 1, 3, 5, 2, 4)

  6. Reverse and Join • Reverse: reverses the order of the elements of the array • @array2 = reverse (@array1) #array2 is (4, 2, 5, 3, 1, 8, 7) • Join collapses an array into a single string • @array1 = (‘Hello’, ‘to’, ‘me.’); • $sentence = join(‘’,@array1); • $sentence is ‘Hello to me.’

  7. Retrieving array length • Using an array in a context where a scalar value is expected returns the length of the array • @array1 = (1, 2, 3, 4); • $a = @array1; #$a is 4

  8. Scalar and List context • Example 4-8 • @bases = (‘A’, ‘C’, ‘G’, ‘T’); • Print “@bases\n”; • Output: A C G T • $a = @bases; • Print $a, “\n”; • Output: 4 • ($a) = @bases; • Print $a, “\n”; • Output: A

  9. Working with Files Biological data can come in a variety of file formats and our job is to utilize these files and extract what we want One such file format is FASTA

  10. Opening a file in Perl • Syntax for open a file in perl: • open (FILEHANDLE, “filename”) or die “Can’t open filename\n”; Open  This is a perl function to open a file FILEHANDLE  The string you use to refer to the file throughout your perl script “filename”  The actual name of the file,double quotes are required Or die “”  tells the program to quit if cannot open or find (optional but recommended)

  11. Closing a file in Perl • Close (FILEHANDLE); • Typically, it is good practice to close a file once you open it…

  12. Scalar vs. Array • Example 4-5 provides a simple distinction between use of a scalar variable and an array, read it, but don’t necessarily do it • Also, it shows how you use filehandles in association with your file • < > are input operators, you will become better acquainted with this when we use <STDIN> later

  13. adhI.pep • Supplant NM_021964fragment.pep with adhI.pep, which can be downloaded from the web-site to a folder you need to create on your computer called “BIOS482” • Do Example 4-7 • Practice manipulating arrays using the code on page 51-53

  14. Flow control • Flow control refers to the order in which the statements of a program is executed • Goes from the first statement at the top to the last statement at the bottom • Unless you implement conditional statements and loops

  15. Statement blocks • A sequence of statements can be grouped together by enclosing them in curly braces {} to form a statement block. Each statement block will be executed in the order in which they appear. • Structure { first statement; last statement; }

  16. Conditional statements • Tests for a condition, which is evaluated as true or false. True conditions lead to the execution of statements, false means they’re skipped (or vice versa) • If-elsif-else (Example 5-1)

  17. Loops • Allows repeated execution of a block of statements enclosed in matching curly braces • While • For • Foreach • Do-while • Until, Etc.

  18. Code Layout • Can be a matter of preference, what you can read well • Some examples are on pg 62 of your text • I would let the examples we do in class help you along the way

  19. Finding motifs • Work through example 5-3 • Read pages 63-70 • Homework

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