BIOS 546 Midterm March 26, Write the line of code that all Perl programs on biolinx must start with so they can be executed.

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Molly Webb
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1 1. What values are false in Perl? BIOS 546 Midterm March 26, Write the line of code that all Perl programs on biolinx must start with so they can be executed. 3. How do you make a comment in Perl? How do you make a comment in HTML? 4. If you are in the /home/bio546 directory, what happens when you give the Unix command "cd.."? 5. What is the difference between "cd /junk" and "cd junk"? 6. What is the internal (biolinx) address of the directory you use to display pages on the internet? What is the external address of this directory (that you would type into the browser)? 7. a. What will: print "The number is $num\n"; give, assuming that $num = 7. b. What will: print 'The number is $num\n'; give, assuming that $num = 7. 8.What is meant by the prefixes: and % in Perl?

2 9. To test whether two scalar variable are equal you can use either "==" or "eq". Under what circumstances would you use one or the other? 10. What does the "chomp" function do? 11. Write statements that will print every item in the on a separate line. 12. Write a statement that will insert the values 2, 4, 6, 8, 10 into an array. Then, write a statement that will remove the first element of the array and put it into $var1. Then write another statement that will remove the last element of the array and put it into $var2. Note: the array should have only 3 elements after all this. 13. If has the values 1,3,5,7 in it, what will the value of $abc be after the statement: $abc

3 14. Write statements that will print all the keys to the hash %hash, sorted in alphabetical order. Also, have your code remove the key-value pair from the hash if the value is less than Write a short program that will prompt the user for a color, then print "YES" if STDIN has a color that is used as a key in the hash %stoplight (i.e. red, yellow, or green), and "NO" if STDIN has some other value. Note that I want you to first create the hash, then test the hash for the presence of those keys 16. Write a regular expression that will match the comment line of a fasta-formatted sequence file: the first character is a ">".

4 17. Modify your expression in 16 above to capture all characters up to the first space, not including the >. Then print out what you have captured Write some code that will find every instance of the word "and" in string $str and replaces it with "or". 19. Write a complete HTML page that contains the following: a. the title "HMTL Page" b. Print a large, centered headline "HEADLINE" c. A short paragraph of text. d A link to e. The picture file "cup.jpg" f. An unordered list consisting of "cat", "dog", "bird" g. A table with 2 rows and 2 columns, with "one" and "two" in the first row, and "three" and "four" in the second row.

5 20. You have 2 = ("dog", "cat", "bird", "fish") = (7, 12, 34, 1) Sort them by age, with oldest first, then print out each pet and its age on a separate line. 21. Write some code that will open $infile and $outfile, then read every line of $infile and print it into $outfile. 22. You have 3 variables: $first = "The", $second = "dog", $third = "runs". Concatenate these into a single variable $fourth that contains "The dog runs". Don't forget the spaces! 23. How would you write the number 1,000,000,000 so it would be readable by the Perl compiler? 24. What does this code do: while (<STDIN>) { print; }

6 25. Create a form that has a text box for entering your name, and a check box (or radio buttons) that convert it to upper case if checked. Also a submit button. The form should send the input to "greet.cgi" in the bios546 sub-directory in the cgi-bin on biolinx. 26 Create the "greet.cgi" program, taking the inputs from 22 above and returning an HTML page that issues a greeting to the person whose name was in the text box, in lower case as the default or in upper case if the checkbox was checked.

7 27. Write a subroutine that takes 2 numbers as input and returns both their sum and their product. Also write a statement that invokes this subroutine and then captures the results. 28. Write a regular expression that will match any character that is NOT a, c, or e, followed by 2 numbers, followed by a *. Remember that * is a metacharacter! 29. On the command line a program is invoked with: "prog2.pl yes 45 fred". How can you get the program to read the second argument (the "45") into the variable $num? 30. Write some statements that will produce the reverse complement of the DNA sequence in $seq.

They grow as needed, and may be made to shrink. Officially, a Perl array is a variable whose value is a list.

Arrays Perl arrays store lists of scalar values, which may be of different types. They grow as needed, and may be made to shrink. Officially, a Perl array is a variable whose value is a list. A list literal