149 lines
5.5 KiB
R
149 lines
5.5 KiB
R
# tocID <- "BIN-MYSPE.R"
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#
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# ---------------------------------------------------------------------------- #
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# PATIENCE ... #
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# Do not yet work wih this code. Updates in progress. Thank you. #
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# boris.steipe@utoronto.ca #
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# ---------------------------------------------------------------------------- #
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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: 1.1
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#
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# Date: 2020-09-18
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# V 1.1 2020 Workflow changes
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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 47
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#TOC> 2 Suitable MYSPE Species 59
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#TOC> 3 Adopt "MYSPE" 83
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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("./myScripts/.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 In brief, data for genome-sequenced fungi
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# was retrieved from https://fungi.ensembl.org; a search for homologues to
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# yeast Mbp1 was performed with BLAST at the NCBI, and the data was merged.
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# A representative organism at each genus-level was chosen from those hits
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# that actual;ly have a homologue. Finally, a mapping table was constructed to
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# asymmetrically retrieve unique species: a student number will retrieve
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# a species, but (public) knowledge of the species cannot reconstruct the
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# student number.
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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 various data resources. Studying
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# it will give you a better sense of how such workflows can be
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# implemented in practice.
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# = 3 Adopt "MYSPE" =======================================================
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# Execute:
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( MYSPE <- getMYSPE(myStudentNumber) )
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# If this produced an error, this session has not been properly set up. You
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# may not yet have run init() and edited .myProfile.R , or that file is not
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# in your myScripts/ folder. Fix this, and execute source(".Rprofile") .
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# If this produced NA, your Student Number may not be correct, or you are not
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# in my class-list. Contact me.
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# Otherwise, this should have printed a species name. Your unique species
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# for this course.
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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 BiCode 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. Whenever you start a session, it will automatically be loaded
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# from myScripts/.myProfile.R and is available as MYSPE .
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# Here is some more information:
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fungiDat <- read.csv("data/Species.csv")
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# number of sequenced fungal genomes:
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nrow(fungiDat)
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# sequenced genomes of species:
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sel <- MYSPE == gsub("^(\\S+\\s\\S+).*$", "\\1", fungiDat$Name)
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( x <- fungiDat[sel, "Name"] )
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Nspc <- length(x) # save this for later ...
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# sequenced genomes of genus:
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sel <- gsub("\\s.*", "", MYSPE) == gsub("\\s.*", "", fungiDat$Name)
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( x <- fungiDat[sel, "Name"] )
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Ngen <- length(x) - Nspc
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# order:
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( x <- unique(fungiDat[sel, "Classification"]) )
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Nord <- sum(fungiDat$Classification == x) - Ngen - Nspc
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Nfng <- nrow(fungiDat) - Nord - Ngen - Nspc
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# proportions
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pCol <- c("#ed394e", "#ff9582", "#ffd5c4", "#f2f2f0")
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oPar <- par(mar = c(1.1, 0, 1.1, 1))
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pie(c(Nspc, Ngen, Nord, Nfng),
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labels = "",
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radius = 1,
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main = "MYSPE in genome-sequenced fungi",
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sub = MYSPE,
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lty = 0, # no borders for wedges
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col = pCol,
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clockwise = TRUE,
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init.angle = 90)
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legend(x = 1.05, y = 0.8, # position
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legend = c("Species", "Genus", "Order", "Fungi"),
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y.intersp = 2, # line spacing for labels
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cex = 0.8, # character size for labels
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bty = "n", # "no" box around the legend
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pt.cex = 2, # size of colour boxes
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pch = 15,
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col = pCol)
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par(oPar)
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# [END]
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