Week 2 Overview: Unix and Perl Exercises, Homework Assignments, and Website Updates

1. CS 451 / 558 Week 2, Thur

2. Misc • Website updates • Homework • Projects

3. In class exercises – Unix 4 • How many words in /usr/share/dict/words? • Print a list of words that contain ‘nj’ • Write that list to a file (do this in a new directory)

4. In class exercises – Unix 5 • Create a new directory • Download sequences.fa • Look at the format of the file • How many sequences are there? • Download .gz version • Unzip it • Is it the same as the other file?

5. In class exercises – Unix 6 • Create a new directory • Use browser to HMMER from hmmer.org • Move the .tar.gz file to your new directory • Unzip the file Creates hmmer-3.1b1-linux-intel-x86_64/ • Look at contents • Make a copy of the entire directory • Remove the original directory

6. Unix side notes • awk, sed, man

7. In class exercises – Perl 1 • Write a program that stores an integer in a variable, then prints it out (4.2 from the book)

8. In class exercises – Perl 2 • Write a program that prints DNA of arbitrary case in lowercase (acgt); write another that prints in upper case (ACGT). (4.3 from the book)

9. In class exercises – Perl 3 • Write a program to reverse transcribe RNA to DNA (4.5 from the book)

10. In class exercises – Perl 4 • Read two files of data (sequence1.fa and sequence2.fa). Print the contents of the first, then the contents of the 2nd. (4.6 from the book)

11. In class exercises – Perl 5 • Write a program to read a file, then print its lines in reverse order (last line first). • Options • reverse • push/pop/shift/unshift (possibly with loops) (4.7 from the book)