PERL (Jan 2011)

Perl course - 17-28 January, 2011

30 hours

FIOCRUZ-Minas / CEBio

Trainers

Adhemar Zerlotini
Eric Aguiar
Francislon Silva

Participants

Armando de Menezes Neto - CPqRR FIOCRUZ
Fabiano Pais - CEBio - FIOCRUZ
Fausto Santos - CEBio - FIOCRUZ
Laura Rabelo - CEBio - FIOCRUZ
Lívia Avelar - CPqRR FIOCRUZ
Lívia Moura - Federal Unviersity of Uberlândia
Luana Torres - Federal Unviersity of Uberlândia
Mariana Oliveira - CEBio - FIOCRUZ
Ricardo S. Ribeiro - CPqRR FIOCRUZ
Sara Cuadros-Orellana - CEBio - FIOCRUZ

Lectures

Lecture 1

Lecture 2

Begining Perl

  • Installing Perl
  • Documentation
  • Your first program
  • Numbers and strings
  • Literal
  • Scalable variables
  • Expressions and operators
  • More operators
  • Exercises

Blocs

  • Conditions(if,else)
  • Looping
  • Other flux commands
  • Receiving values in the command line (GetOpt)
  • Exercises

Lecture 3

Lecture 4

Placing values in lists and arrays

  • Returning elements in arrays
  • Manipulating arrays
  • Exercises
  • Hashes
  • Loading your Hash
  • Returning data in a Hash
  • Lists and Hashes
  • Interesting Hash applications
  • Exercises

Simple patterns

  • Metacharacters
  • Substitution
  • Finding other patterns
  • Exercises

Lecture 5

Lecture 6

Working with files

  • Opening files
  • Reading files
  • Free files, testing files and binary data
  • Exercises

Functions

  • Creating and calling subroutines
  • Scope
  • Exercises
  • Footnote function
  • Exercises

Lecture 7

Lecture 8

CPAN

  • Installing modules DBI and DBD::mysql
  • Instanciating classes and using your methods
  • Connecting to a database
  • Insert
  • Select
  • Exercises

BioPerl

  • Iniciation into BioPerl
  • Installing BioPerl
  • Documentation
  • Reading FASTA files
  • Counting the number of sequences in a file
  • Counting the number of bases in a file
  • Counting the number of bases ignoring certain characters
  • Identifying motifs in a file
  • Exercises

Lecture 9

Lecture 10

BioPerl - Reading annotation files (BenBank / EMBL)

  • Counting the number of sequences in a file
  • Counting the number of bases in a file
  • Counting the number of bases ignoring certain characters
  • Identifying motifs in a file
  • Writing files
  • Converting file formats
  • Working with compacted files
  • Exercises

BioPerl - Extracting sequences by ID

  • Extracting and locating sequences by ID
  • Reading Blast files
  • Filtering Blast files
  • Exercises