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

References

Subroutines


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

Phyml

EMBOSS


24 February 2010

Object-oriented programming in Perl

Installing Bioperl


25 February 2010

Bio::SeqIO

Bio::Seq