Recorded Videos
1. Introduction to Unit 2 of BCH519
4 mins
2. Introduction to Linux
7 mins
3. Remotely connecting to CCR
7 mins
4. Linux Command Line Boot Camp
23 mins
5. Python Language Overview
34 mins
6. Python Functions and STL
14 mins

7. Python File IO
Lecture Slides
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!