89 lines
3.2 KiB
R
89 lines
3.2 KiB
R
# BIN-MYSPE.R
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the BIN-MYSPE unit
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#
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# Version: 1.0.1
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#
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# Date: 2017 09 21
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 1.0.1 Move ABC-makeMYSPElist.R to ./scripts directory
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# V 1.0 Final code, after rewriting BLAST parser and updating MYSPElist
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# V 0.1 First code copied from BCH441_A03_makeMYSPElist.R
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#
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# TODO:
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#
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#
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# == HOW TO WORK WITH LEARNING UNIT FILES ======================================
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#
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# DO NOT SIMPLY source() THESE FILES!
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> -----------------------------------------------
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#TOC> 1 Preparations 39
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#TOC> 2 Suitable MYSPE Species 51
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#TOC> 3 Adopt "MYSPE" 65
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#TOC>
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#TOC> ==========================================================================
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# = 1 Preparations ========================================================
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#
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# Execute the two conditionals below:
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if (! file.exists(".myProfile.R")) {
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stop("PANIC: profile file does not exist. Fix problem or ask for help.")
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}
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if (! exists("myStudentNumber")) {
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stop("PANIC: profile data wasn't loaded. Fix problem or ask for help.")
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}
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# = 2 Suitable MYSPE Species ==============================================
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# In this unit we will select one species from a list of genome sequenced fungi
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# and write it into your personalized profile file. This species will be called
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# "MYSPE" (Your Favourite Organism) for other learning units and exercises.
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# A detailed description of the process of compiling the list of genome
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# sequenced fungi with protein annotations and Mbp1 homologues is in the file
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# ./scripts/ABC-makeMYSPElist.R
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# Task: Study ./scripts/ABC-makeMYSPElist.R, it implements a typical workflow
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# of selecting and combining data from public-domain data resources.
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# = 3 Adopt "MYSPE" =======================================================
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# In the code below, we load the resulting vector of species name, then pick one
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# of them in a random but reproducible way, determined by your student number.
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load("data/MYSPEspecies.RData") # load the species names
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set.seed(myStudentNumber) # seed the random number generator
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MYSPE <- sample(MYSPEspecies, 1) # pick a species at random
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set.seed(NULL) # reset the random number generator
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# write the result to your personalized profile data so we can use the result in
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# other functions
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cat(sprintf("MYSPE <- \"%s\"\n", MYSPE), file = ".myProfile.R", append = TRUE)
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MYSPE # so, which species is it ... ?
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biCode(MYSPE) # and what is it's "BiCode" ... ?
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# Task: Note down the species name and its five letter label on your Student
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# Wiki user page. Use this species whenever this or future assignments refer
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# to MYSPE. In code, we will automatically load it from your .myProfile.R file.
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# [END]
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