Difference between revisions of "RPR-FASTA"

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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
 
FASTA files with R
 
FASTA files with R
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(R coding for the FASTA format and its aligned and multi-FASTA variants)
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<div class="keywords">
 
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<b>Keywords:</b>&nbsp;
 
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R coding for the FASTA format and its aligned and multi-fasta variants
 
 
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{{Smallvspace}}
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__TOC__
 
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{{STUB}}
 
  
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<div style="font-size:118%;">
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<b>Abstract:</b><br />
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== Abstract ==
 
 
<section begin=abstract />
 
<section begin=abstract />
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "abstract" -->
 
 
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.
 
<section end=abstract />
 
<section end=abstract />
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<!-- ============================ -->
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<hr>
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<table>
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== This unit ... ==
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<tr>
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=== Prerequisites ===
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<td style="padding:10px;">
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "prerequisites" -->
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<b>Objectives:</b><br />
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You need to complete the following units before beginning this one:
 
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*[[BIN-Sequence|BIN-Sequence (Sequence)]]
 
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=== Objectives ===
 
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "objectives" -->
 
 
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;
 
* ... teach how to read, process and write FASTA formatted files;
 
* ... teach how to read, process and write FASTA formatted files;
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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=== Outcomes ===
 
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "outcomes" -->
 
 
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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* ... are familar with a number of pittfalls of doing so;
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* ... are familar with a number of pitfalls of doing so;
 
* ... can write code to analyze the sequences you have read;
 
* ... 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.
 
* ... can write code to write the sequences to the console or to a file in chunks of defined width.
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<!-- ============================  -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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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>
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<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>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-Sequence|BIN-Sequence (Sequence)]]
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<section end=prerequisites />
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<!-- ============================  -->
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=== Deliverables ===
 
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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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.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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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]].
 
  
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=== Evaluation ===
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__TOC__
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "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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=== Evaluation ===
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<div id="BIO">
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
 
== Contents ==
 
== Contents ==
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<!-- included from "../components/RPR-FASTA.components.wtxt", section: "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.
 
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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== Further reading, links and resources ==
 
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== Notes ==
 
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<references />
 
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== Self-evaluation ==
 
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<b>If in doubt, ask!</b> 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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<div class="about">
 
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:2017-08-05
 
:2017-08-05
 
<b>Modified:</b><br />
 
<b>Modified:</b><br />
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:2017-08-05
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:2020-09-23
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:1.0
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:1.0.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.0.1 2020 maintenance
 
*1.0 First live version
 
*1.0 First live version
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 08:51, 24 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.

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.

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


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    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.


     


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-23

    Version:

    1.0.1

    Version history:

    • 1.0.1 2020 maintenance
    • 1.0 First live version
    • 0.1 First stub

    CreativeCommonsBy.png This copyrighted material is licensed under a Creative Commons Attribution 4.0 International License. Follow the link to learn more.

    Retrieved from "http://steipe.biochemistry.utoronto.ca/abc/index.php?title=RPR-FASTA&oldid=11630"