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add biopython example code; add course table of contents to help planning for teachers
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‎TOC.md‎

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An Introduction to Solving Biological Problems with Python
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================================================================================
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Divided into 4 sessions over two days.
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1. DAY 1. MORNING. SESSION 1.: running the Python interpreter, variables and types, arithmetic, basic data structures
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2. DAY 1. AFTERNOON. SESSION 2.: logic & flow control, loops, exceptions, importing libraries
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3. DAY 2. MORNING. SESSION 3.: custom functions, variable scope, some biological examples
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4. DAY 2. AFTERNOON. SESSION 4.: dealing with files, parsing file formats, introduction to BioPython
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DAY 1. MORNING. SESSION 1.
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--------------------------------------------------------------------------------
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### Part 1. [Gabor]
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INTRO: the python programming language & python interpreter (command line)
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Python is free, cross-platform, widely used, well documented & well supported.
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Python is a simple interpreted language, with no separate compilation step.
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- Getting started
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- Printing values
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- Using variables: they are names for values, created by use. No declaration necessary.
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A variable is just a name, it does not have a type. Values are garbage collected,
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if nothing refers to data any longer, it can be recycled. Must assign value to variable
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before using it. Python does not assume default values for variables,
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doing so can mask many errors.
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- Simple data types: Values do have types. Use functions to convert between types.
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- booleans
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- integers
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- floating point numbers
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- complex numbers
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- strings are sequences of characters
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- the None object
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- Arithmetic: addition, subtraction, multiplication, division, exponentiation, remainder
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- Saving code in files
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- Comments
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#### EXERCISES
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```
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* create a variable, print out a message
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* addition operator
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* calculate the mean of two variables
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* [1.1] Print DNA sequence from amino acid one.
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```
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### Part 2. [Anne]
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As well as the basic data types we introduced, python has several ways of storing
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a collection of values. We are going to see four of them: tuples, lists, sets and
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dictionaries.
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- Collections: complex data types
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- tuples: A tuple is a sequence of immutable Python objects. Tuples are sequences,
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just like lists. The only difference is that tuples can't be changed i.e.,
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tuples are immutable and tuples use parentheses and lists use square brackets.
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- lists: the most popular [value, value, value, ...] it is mutable, it can be
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changed after been created. It is heterogeneous, it can store values of many kinds.
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Appending values to a list lengthens it, deleting values shortens it. Most
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operations on lists are methods. Two that are often used incorrectly sort() and reverse()
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- manipulating tuples and lists
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Online Python doc: https://docs.python.org/2/ Library | 5.6. Sequence Types | Mutable Sequence Types (5.6.4)
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#### EXERCISES
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```
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* [1.2] Print DNA sequence from a list of DNA codons
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```
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- String manipulations and format: strings are indexed exactly like lists.
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Strings are immutable, they cannot be changed in place. Use + to concatenate strings.
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Concatenation always produces a new string. Use string % to format output.
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Use triple quotes for multi-line strings. Strings have methods: capitalize()
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upper() lower() count() find() replace()
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Online Python doc: https://docs.python.org/2/ Library | 5.6. Sequence Types | 5.6.1. String Methods
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Online Python doc: https://docs.python.org/2/ Library | 5.6. Sequence Types | 5.6.2. String Formatting Operations
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#### EXERCISES
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```
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* [1.3] String manipulation using your name
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```
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- Sets contain unique unordered elements. They are very similar to lists but
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because the elements are not in order they do not have an index.
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Online Python doc: https://docs.python.org/2/ Library | 5.7. Set Types
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#### EXERCISES
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```
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* [1.4] Find the unique amino acid codes in a protein sequence
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```
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- Dictionaries contain a mapping of keys to values
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Online Python doc: https://docs.python.org/2/ Library | 5.8. Mapping Types
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```
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Dictionary can be very useful when combined with string formatting e.g.
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format_string = "Dear %(name)s, we have sequenced %(num)d libraries. The yield is %(yield)dM reads."
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print format_string % {'name': 'Anne', 'num':3, 'yield': 182}
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```
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#### EXERCISES
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```
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* [1.5] Use a dictionary to map between codon sequences and amino acids they
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encode to print out the name of the amino acids of a DNA sequence
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```
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```
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>>> TAKE HOME MESSAGE
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>>> Variables are labels that refer to data.
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>>> Many variables may refer to the same piece of data.
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>>> Use strings to store text.
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>>> Use lists to store many related values in order.
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>>> User sets to store unique related values in order.
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>>> Use dictionaries to store key/value pairs.
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```
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DAY 1. AFTERNOON. SESSION 2.
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--------------------------------------------------------------------------------
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### Part 1. [Gabor]
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INTRO: program control and logic - code blocks: if/loops/exceptions.
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Real power of programs comes from repetition and selection. Why indentation?
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Because it makes the code you write clearer and easier to read.
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Python style guide (PEP 8) recommends 4 spaces.
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Loops let us do things many times. Collections let us store many values together.
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- code blocks
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- conditional execution
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- the if statement: use if/elif/else to make choices
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- comparisons and truth
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#### EXERCISES
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```
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[2.0] Compare your age with other persons and print if you are younger/older/same age
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[2.?] Check if a DNA sequence contain a stop codon
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```
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- loops
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- the for loop: a for loop is used to access each value in turn
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- the while loop: a while loop is used to step through all possible indices
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- skipping and breaking loops
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- looping gotchas
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#### EXERCISES
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```
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[2.1] Loop over a list of bases using for and while loops
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```
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- more looping
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- using enumerate
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- using zip
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- filtering in loops
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#### EXERCISES
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```
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[2.2] Calculate the GC content of a DNA sequence
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```
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### Part 2 (after break) [Anne]
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Python provides two very important features to handle any unexpected error in your
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Python programs and to add debugging capabilities in them: exceptions and assertions.
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- exceptions: An exception is an event, which occurs during the execution of a program,
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that disrupts the normal flow of the program's instructions. In general, when a Python
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script encounters a situation that it can't cope with, it raises an exception.
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An exception is a Python object that represents an error.
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#### EXERCISES
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```
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[2.3] Raise an exception if the DNA sequence is not valid
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```
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- importing modules and libraries
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- help(math)
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- import sys
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- print sys.version & sys.platform
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- print sys.path which defines the list of directories Python searches in to find modules.
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sys.argv: The most commonly-used element of sys is probably sys.argv, which holds the command-line arguments of the currently-executing program.
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```
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>>> TAKE HOME MESSAGE
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>>> Use while to repeat something until something changes.
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>>> Use for to do something once for each part of a larger whole.
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>>> Use if and else to make choices.
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```
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DAY 2. MORNING. SESSION 3.
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--------------------------------------------------------------------------------
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### Part 1. [Anne]
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INTRO: function basics and definition
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A programming language should not include everything anyone might ever want
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Instead, it should make it easy for people to create what they need
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to solve specific problems by defining functions to create higher-level operations.
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In python it is done using the keyword 'def'.
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- function definition syntax
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#### EXERCISES
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```
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[3.1a] Create a function that calculate the means of two number and then from a list of number
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[3.1b] Create a function to calculate the molecular weight of a DNA sequence
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```
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- function arguments
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#### EXERCISES
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```
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[3.2] Extend the previous function to also calculate the weight of a RNA sequence
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```
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- return value
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#### EXERCISES
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```
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[3.3] Write a function that counts the number of each base found in a DNA sequence
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```
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### Part 2. [Gabor]
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- variable scope: globals vs within blocks
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- advanced topics: anonymous functions (lambda); functions as values; nested functions
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#### EXERCISES
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```
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BIO examples
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- program ribosome that translates RNA into protein
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- extra points for also taking DNA (T -> U)
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- extra points for all reading frames.
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- calculate GC content of DNA not on whole sequence but with sliding window.
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- calculate hydrophobicity with sliding window.
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```
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```
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>>> TAKE HOME MESSAGE
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>>> Define functions to break programs down into manageable pieces.
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>>> Remember that a function is really just another kind of data.
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```
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Day 2. AFTERNOON. SESSION 4.
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--------------------------------------------------------------------------------
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### Part 1. [Anne]
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INTRO: In this session we cover 2 widely used ways of reading data into our
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programs, via the command line and by reading files from disk.
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- reading command line arguments
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#### EXERCISES
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```
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[4.1a] Write a script that takes 2 integers from the command line using the sys.argv
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library, add the two numbers and printout the result
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[4.1b] Write a script tha takes a DNA sequence from the command line and prints out
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its length and GC content
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```
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- the argparse library
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#### EXERCISES
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```
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[4.1c] Use the argparse library to do the same exercise as above
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```
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### Part 2. [Gabor]
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- file objects
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- mode modifiers
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- error checking
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- closing files
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- reading from files
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- the with statement
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- writing to files
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#### EXERCISES
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```
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[4.2a] Write a script that writes a list of number to a file, with each number
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on a separate line
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[4.2b] Open a file and for each line print out the line number and its length
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```
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- data formats
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- delimited files
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- reading delimited files
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- writing delimited files
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- more advanced examples
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- read csv file
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- write csv file
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#### EXERCISES
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```
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[4.3a] Read a tab separated file
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[4.3b] Write a csv file
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```
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- fixed format files (PDB)
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- XML files
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- python file libraries: os & os.path
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- more advanced examples
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- recursive file search
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- recursive delete
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- system calls
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#### EXERCISES
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```
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[4.4] Write a script that execute the command 'ls' to get the list of files
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then modify your script to only print python files
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```
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### Part 3. [Anne]
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- using BioPython
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Biopython is to make it as easy as possible to use Python for bioinformatics by
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creating high-quality, reusable modules and classes. Biopython features include
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parsers for various Bioinformatics file formats (BLAST, Clustalw, FASTA, Genbank,...),
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access to online services (NCBI, Expasy,...), interfaces to common and not-so-common programs
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(Clustalw, DSSP, MSMS...), a standard sequence class, various clustering modules,
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a KD tree data structure etc. and even documentation.
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Basically, we just like to program in Python and want to make it as easy as possible
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to use Python for bioinformatics by creating high-quality, reusable modules and scripts.
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Biopython tutorial http://biopython.org | Tutorial | 1.2 What can I find in the Biopython package
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#### BioPython EXAMPLES
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- more advanced examples
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- writing FASTA files
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- reading FASTA files
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```
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>>> TAKE HOME MESSAGE
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>>> Happy Python programming!
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```
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IDEAS: if you need help: http://stackoverflow.com/
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IDEAS: Pylint is a tool that checks for errors in python code, tries to enforce a coding standard and looks for bad code smells: http://www.pylint.org/
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IDEAS: Any code that hasn't been tested is probably wrong: Python unit testing framework unittest
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IDEAS: from http://software-carpentry.org/v4/python

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