Difference between revisions of "RPR-FASTA"
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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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FASTA files with R | FASTA files with R | ||
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(R coding for the FASTA format and its aligned and multi-fasta variants) | (R coding for the FASTA format and its aligned and multi-fasta variants) | ||
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| − | + | <li><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.</li> | |
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" --> | <!-- included from "./data/ABC-unit_components.txt", section: "deliverables-journal" --> | ||
| − | + | <li><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.</li> | |
<!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" --> | <!-- included from "./data/ABC-unit_components.txt", section: "deliverables-insights" --> | ||
| − | + | <li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li> | |
<section end=deliverables /> | <section end=deliverables /> | ||
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| − | This unit builds on material covered in the following prerequisite units: | + | This unit builds on material covered in the following prerequisite units:<br /> |
*[[BIN-Sequence|BIN-Sequence (Sequence)]] | *[[BIN-Sequence|BIN-Sequence (Sequence)]] | ||
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Revision as of 12:40, 16 September 2020
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:
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Outcomes:
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Deliverables:
Prerequisites:
This unit builds on material covered in the following prerequisite units:
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-unitsR 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.Rand 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
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
This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.
