Unit 2 Linux/Python

1. Video Recordings 2. Outline for this lecture 3. What is an Operating System 4. Operating Systems 5. UNIX History 6. UNIX 7. UNIX Features 8. UNIX Philosophy 9. UNIX Descendents 10. Linux 11. Linux 12. Many flavors of Linux 13. Linux on the Desktop 14. Linux in the Data Center 15. Linux is Everywhere 16. Why Linux for this Course? 17. Getting started with Linux 18. Linux - Remote Login 19. CCR OnDemand 20. CCR OnDemand 21. CCR OnDemand Shell 22. Operating systems user interfaces 23. CLI - Command Line Interface 24. Anatomy of the shell 25. How to read the SHELL 26. Anatomy of a command 27. Command Line Boot Camp 28. Simple Commands 29. Simple Commands 30. Getting Help 31. Download and print! 32. Files, Directories, and Paths 33. Hierarchical Filesystem 34. Moving around 35. File Basics 36. Text Manipulation 37. Input/Output redirection 38. Pipes 39. Editing Files 40. Editors 41. GNU nano 42. GNU nano basics 43. GNU nano 44. Homework #1

1. Video Recordings 2. Outline for this lecture 3. Text Manipulation 4. Input/Output redirection 5. Pipes 6. Find 7. sed 8. Using paste 9. Using paste continued.. 10. AWK: Versatile Scripting 11. AWK: Example 12. AWK: Sample Scripts 13. Examples using real data 14. Parsing Cufflinks Gene Expression 15. Cutting cufflinks tables 16. Sorting the temp files 17. Pasting cufflinks temp files 18. Viewing the Table 19. Reformatting Files using Linux 20. UCSC File Format Resource 21. FIMO to BED Format 22. Format Exercise: Fimo to Bed 23. Format Exercise: Fimo to Bed 24. Sorting Data 25. In-Class Exercises 26. Homework #1

1. Course Goals 2. Book 3. What is Python? 4. Programming in Python 5. Running Python programs 6. Python versions 7. Python Documentation 8. Code to all exercises 9. Basic Syntax Overview 10. Exercise 1: First Python Program 11. What do errors look like? 12. Exercise 1: What we learned 13. Exercise 2: Comments 14. Exercise 2: What we learned 15. Exercise 3: Numbers 16. Exercise 3: What we learned 17. Exercise 4: Variables 18. Exercise 4: What we learned 19. Exercise 5: Strings 20. Exercise 5: Output 21. Exercise 5: What we learned 22. Exercise 6: Printing Strings 23. Exercise 6: Output 24. Exercise 6: What we learned 25. Control Structures 26. Conditionals 27. Basic structure of the if statement 28. Exercise 7: Conditionals 29. Exercise 7: Output 30. Example flow control 31. Boolean Logic 32. Exercise 8: Boolean Operators 33. Exercise 7 & 8: What we learned 34. Python builtin operators 35. Loops 36. Basic structure of looping constructs 37. Example flow control 38. Exercise 9: Loops 39. Exercise 9: Output 40. Exercise 10: Nesting loops 41. Exercise 9 & 10: What we learned 42. Executing Python programs 43. Homework #2

1. Topics Covered 2. The Python Standard Library and Built-in Functions 3. What is a function? 4. Python has many built-in functions 5. What is a module? 6. The Python Standard Library 7. Exercise 1: Modules and functions 8. Exercise 1: Output 9. Exercise 1: What we learned 10. Defining Functions 11. Exercise 2: Functions 12. Exercise 2: Output 13. Exercise 2: What we learned 14. Data Structures 15. Lists 16. Exercise 3: Accessing List Values 17. Exercise 3: Output 18. Exercise 3: What we learned 19. Dictionaries 20. Exercise 4: Accessing Dict items 21. Exercise 4: Output 22. Exercise 4: What we learned 23. Printing and manipulating text 24. Calculating AT content 25. Calculating AT content Solutions 26. Complementing DNA 27. Complementing DNA solutions 28. Complementing DNA solutions 29. Restriction fragment lengths 30. Restriction fragment lengths solutions 31. Splicing out introns, part one 32. Splicing out introns part 1 solutions 33. Splicing out introns, part two 34. Splicing out introns part 2 solutions 35. Splicing out introns, part three 36. Splicing out introns part 3 solutions 37. Homework #2

1. Topics Covered 2. Command Line Arguments 3. Passing arguments to python script 4. The special list: sys.argv 5. Exercise 1: echo in python 6. Exercise 1: What we learned 7. Exercise 2: add two numbers 8. Exercise 2: What we learned 9. File I/O 10. Files 11. File Objects 12. sys.stdout = Standard Output 13. Opening and closes files 14. Writing to Files 15. Reading Files 16. Reading Files Example Code 17. sys.in = Standard Input 18. Typical I/O Scenario 19. Exercise 3: cat in python 20. Exercise 4: grep in python 21. Exercise 4: grep in python output 22. Exercise 3 & 4: What we learned 23. Modules 24. What is a Module? 25. Simple Python module example 26. How to use Python modules? 27. PyPI 28. Example: Biopython 29. Parsing FASTA files 30. Exercise 5: Parsing FASTA files with Biopython 31. Debugging - pprint 32. Exercise 6: pprint 33. Homework #3

1. Topics Covered 2. Python Interactive Mode 3. Python Virtual Environments 4. Parsing command line arguments 5. Parsing data using data structures 6. Parsing data 7. Parsing data using data structures 8. Reading and Writing Files 9. Splitting genomic DNA 10. Splitting genomic DNA 11. Lists and Loops 12. Processing DNA in a file 13. Processing DNA in a file 14. Multiple exons from genomic DNA 15. Multiple exons from genomic DNA 16. Writing our own functions 17. Percentage of amino acid residues, part 1 18. Percentage of amino acid residues, part 1 19. Percentage of amino acid residues, part 2 20. Percentage of amino acid residues, part 2 21. Happy Python Hacking!