Bioperl introductionary training
Contents
- 1 Bioperl
- 2 Training outline
- 3 Exercises
- 3.1 Day 1
- 3.1.1 Bioperl Training Exercise 1: perldoc
- 3.1.2 Bioperl Training Exercise 2: thou shalt not forget
- 3.1.3 Bioperl Training Exercise 3: arrays
- 3.1.4 Bioperl Training Exercise 4: hashes
- 3.1.5 Bioperl Training Exercise 5: packages and modules 1
- 3.1.6 Bioperl Training Exercise 6: packages and modules 2
- 3.1.7 Bioperl Training Exercise 7: complex data structures
- 3.1.8 Bioperl Training Exercise 8: OOP
- 3.1.9 Bioperl Training Exercise 9: inheritance, polymorphism
- 3.1.10 Bioperl Training Exercise 10: aggregation, delegation
- 3.2 Scratch pad
- 3.3 Day 2
- 3.3.1 Bioperl Training Exercise 11: IO, add annotation, run EMBOSS application
- 3.3.2 Bioperl Training Exercise 12: Create a fuzzpro processor module
- 3.3.3 Bioperl Training Exercise 13: Create a taxon processor module
- 3.3.4 Bioperl Training Exercise 14: Create a reference processor module
- 3.3.5 Bioperl Training Exercise 15: Magical processor module
- 3.1 Day 1
- 4 References, Sources, ...
- 5 Author
- 6 Inspired by
Bioperl
Bioperl is a collection of perl modules that facilitate the development of perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces (eg Entrez, SRS) do. On the other hand, bioperl does provide reusable perl modules that facilitate writing perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.
Training outline
See [1]
Exercises
Day 1
Bioperl Training Exercise 1: perldoc
Bioperl Training Exercise 2: thou shalt not forget
Bioperl Training Exercise 3: arrays
Bioperl Training Exercise 4: hashes
Bioperl Training Exercise 5: packages and modules 1
Bioperl Training Exercise 6: packages and modules 2
Bioperl Training Exercise 7: complex data structures
Bioperl Training Exercise 8: OOP
Bioperl Training Exercise 9: inheritance, polymorphism
Bioperl Training Exercise 10: aggregation, delegation
Scratch pad
- references: create a module containing a subroutine to sort arrays on length. Show Schwartzian Tranform solution as well.
- A pragma is a module which influences some aspect of the compile time or run time behaviour of Perl. e.g. use strict
Day 2
- bioperl ships with a whole bunch of ready to use scripts. They all start with bp_. On the command line type bp_ <tab> to list them all.
- use regular perldoc for information, e.g. perldoc bp_split_seq
- scripts that might be useful:
- bp_sreformat:sequence and alignment format conversion. bp_seqconvert is similar but only allows sequence conversions.
- bp_search2table: generate table output from e.g. blast report
- bp_taxid4species: return a list of taxa ids for requested organisms
- bp_mutate: randomly mutagenize a single protein or DNA sequence
- etc ...
Bioperl Training Exercise 11: IO, add annotation, run EMBOSS application
Bioperl Training Exercise 12: Create a fuzzpro processor module
Bioperl Training Exercise 13: Create a taxon processor module
Bioperl Training Exercise 14: Create a reference processor module
Bioperl Training Exercise 15: Magical processor module
References, Sources, ...
Dependencies
- Class::Inspector
- Getopt::long
- pod::usage
- perltidy
- Geany
- EMBOSS
Author
Marc Logghe
Inspired by
- Probably the best Perl book in the world: Object Oriented Perl by Damian Conway.
- Randal Schwartz's Perls of Wisdom
- Perl Training Australia
