RPR-FASTA

FASTA files with R

(R coding for the FASTA format and its aligned and multi-fasta variants)

 

Abstract:

FASTA is file format for sequence data. In this unit we show reading, interpreting and writing FASTA data.

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Objectives: This unit will ... ... introduce the FASTA format and some of its quirks and variations; ... teach how to read, process and write FASTA formatted files;

Outcomes: After working through this unit you ... ... can write code to read FASTA and multi-FASTA files; ... are familar with a number of pitfalls of doing so; ... can write code to analyze the sequences you have read; ... can write code to write the sequences to the console or to a file in chunks of defined width.

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Deliverables:

Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.

Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.

Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

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Prerequisites:
This unit builds on material covered in the following prerequisite units:

• BIN-Sequence (Sequence)

 

This page is tagged for revision; expect changes and proceed with caution.

 

 

Contents

The FASTA format is a text-based, compact format for nucleotide or protein sequences. Due to its simple, compact structure, it is ubiquitous in bioinformatics.

Task:

 

• Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
• Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
• Type init() if requested.
• Open the file RPR-FASTA.R and follow the instructions.

 

Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.

 

Self-evaluation

Notes

Further reading, links and resources

 

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If in doubt, ask! If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.

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About ...
 
Author:

Boris Steipe <boris.steipe@utoronto.ca>

Created:

2017-08-05

Modified:

2017-08-05

Version:

1.0

Version history:

• 1.0 First live version
• 0.1 First stub

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