Difference between revisions of "RPR-FASTA"

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== Abstract ==
 
== Abstract ==
 
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<section begin=abstract />
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FASTA is file format for sequence data. In this unit we show reading, interpreting and writing FASTA data.
 
FASTA is file format for sequence data. In this unit we show reading, interpreting and writing FASTA data.
 
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== This unit ... ==
 
== This unit ... ==
 
=== Prerequisites ===
 
=== Prerequisites ===
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You need to complete the following units before beginning this one:
 
You need to complete the following units before beginning this one:
 
*[[BIN-Sequence|BIN-Sequence (Sequence)]]
 
*[[BIN-Sequence|BIN-Sequence (Sequence)]]
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=== Objectives ===
 
=== Objectives ===
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This unit will ...
 
This unit will ...
 
* ... introduce the FASTA format and some of its quirks and variations;
 
* ... introduce the FASTA format and some of its quirks and variations;
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=== Outcomes ===
 
=== Outcomes ===
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After working through this unit you ...
 
After working through this unit you ...
 
* ... can write code to read FASTA and multi-FASTA files;
 
* ... can write code to read FASTA and multi-FASTA files;
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=== Deliverables ===
 
=== Deliverables ===
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*<b>Time management</b>: 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.
 
*<b>Time management</b>: 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.
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
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=== Evaluation ===
 
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<b>Evaluation: NA</b><br />
 
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:This unit is not evaluated for course marks.
 
  
 
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<div id="BIO">
 
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== Contents ==
 
== Contents ==
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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.
 
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.
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== Notes ==
 
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<references />
 
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== Self-evaluation ==
 
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[[Category:ABC-units]]
 
[[Category:ABC-units]]
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{{CC-BY}}
 
{{CC-BY}}

Revision as of 01:26, 6 January 2018

FASTA files with R


 

Keywords:  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.


 


This unit ...

Prerequisites

You need to complete the following units before beginning this one:


 


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.


 


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.


 


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.


 


 


Further reading, links and resources

 


Notes


 


Self-evaluation

 



 



 

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.


 

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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