Class index

10 November 2009

Getting started

Moving around the file system using Unix commands

Running a Perl script

The bare bones of a Perl script

Planning a Perl script

12 November 2009

Scalars and arrays

Reading data from an input file

Splitting strings into arrays

17 November 2009

Using while loops to read in multiple lines from a file

Printing to an output file

If/else and unless statements, and comparisons of scalars

19 November 2009

Variable scope

Counting things

24 November 2009

Adding and removing elements from arrays

Sorting arrays of numbers or strings

26 November 2009

Finding the length of an array

Printing arrays using join

1 December 2009

Doing something to every element of an array with a foreach loop

3 December 2009

Introduction to hashes

Naming hashes, and assigning values to them

8 December 2009

Getting a list of the keys of a hash

Doing something to each key-value pair in a hash, using foreach

10 December 2009

Sorting hashes by key or by value

Another option: the values function

15 December 2009

Using keys from one hash to acess the values of another hash

Checking whether a hash value exists and is defined

Finding the intersection/union/differences of two or more lists, and the unique elements of a list

Counting up multiple classes of things

6 January 2010

A few optional revision exercises

12 January 2010

Pattern matching with regular expressions

14 January 2010

Substring capture with regular expressions

Substitution and transliteration

27 January 2010

String concatenation

28 January 2010

Substring manipulation

Operating on numbers

For loops I

2 February 2010

For loops II

4 February 2010



9 February 2010

Making a library of your subroutines

Complex data structures: introduction

Accessing data in complex data structures

11 February 2010

Looping across complex data structures

Adding data to complex data structures

16 February 2010

Sorting complex data structures

Command line programs: the PATH environment variable

Command line programs: installing and running ClustalW

System commands

System commands to move around and modify the file system

23 February 2010

Intro to what's coming up

Local (standalone) BLAST (plus @ARGV)

t_coffee multiple alignment program

Gblocks alignment trimmer



24 February 2010

Object-oriented programming in Perl

Installing Bioperl

25 February 2010