Maintenance
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hyginn
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@ -1,20 +1,15 @@
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# tocID <- "FND-Genetic_code.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 FND-Genetic_code unit.
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#
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# Version: 1.1
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# Version: 1.2
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#
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# Date: 2017 10 - 2019 01
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.2 2020 Maintenance
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# 1.1 Change from require() to requireNamespace(),
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# use <package>::<function>() idiom throughout,
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# use Biocmanager:: not biocLite()
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@ -51,20 +46,26 @@
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# = 1 Storing the genetic code ============================================
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# The genetic code maps trinucleotide codons to amino acids. To store it, we
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# need some mechanism to associate these two informattion items. The most
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# need some mechanism to associate the two representations. The most
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# convenient way to do that is a "named vector" which holds the amino acid
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# code and assigns the codons as names to its elements.
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x <- c("M", "*")
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names(x) <- c("ATG", "TAA")
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x <- c("M", "H", "H", "*", "*", "*")
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names(x) <- c("ATG", "CAC", "CAT", "TAA", "TAG", "TGA")
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x
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# Then we can access the vector by the codon as name, and retrieve the
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# amino acid.
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# amino acid ...
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x["ATG"]
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x["CAC"]
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x["TAA"]
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# ... or the names of elements, to retrieve the codon(s)
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names(x)[x == "M"]
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names(x)[x == "H"]
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names(x)[x == "*"]
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# == 1.1 Genetic code in Biostrings ========================================
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@ -103,33 +104,33 @@ Biostrings::getGeneticCode("12") # Alternative Yeast Nuclear
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# to a "local" variable, rather than retrieving it from the package all the
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# time.
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genCode <- Biostrings::GENETIC_CODE
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GC <- Biostrings::GENETIC_CODE
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# This is a named vector of characters ...
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str(genCode)
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str(GC)
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# ... which also stores the alternative initiation codons TTG and CTG in
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# an attribute of the vector. (Alternative initiation codons sometimes are
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# used instead of ATG to intiate translation, if if not ATG they are translated
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# with fMet.)
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# used instead of ATG to intiate translation, if translation is not initiated
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# at ATG thses are still translated with fMet.)
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attr(genCode, "alt_init_codons")
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attr(GC, "alt_init_codons")
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# But the key to use this vector is in the "names" which we use for subsetting
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# the list of amino acids in whatever way we need.
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names(genCode)
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names(GC)
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# The translation of "TGG" ...
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genCode["TGG"]
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GC["TGG"]
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# All stop codons
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names(genCode)[genCode == "*"]
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names(GC)[GC == "*"]
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# All start codons
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names(genCode)[genCode == "M"] # ... or
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c(names(genCode)[genCode == "M"],
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attr(genCode, "alt_init_codons"))
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names(GC)[GC == "M"] # ... or
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c(names(GC)[GC == "M"],
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attr(GC, "alt_init_codons"))
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# == 2.1 Translate a sequence. =============================================
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@ -148,7 +149,7 @@ mbp1 <- readLines("./data/S288C_YDL056W_MBP1_coding.fsa")
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# The reason for this is that the last character of the file is the letter "A"
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# and not a "\n" line break. This file is exactly how it was sent from the
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# server; I think good, defensive programming practice would have been to
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# NCBI server; I think good, defensive programming practice would have been to
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# include some kind of an end-marker in the file, like a final "\n". This helps
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# us recognize an incomplete transmission. Let's parse the actual sequence from
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# the file, and then check for completeness.
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@ -187,7 +188,7 @@ head(mbp1Codons)
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mbp1AA <- character(834)
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for (i in seq_along(mbp1Codons)) {
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mbp1AA[i] <- genCode[mbp1Codons[i]]
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mbp1AA[i] <- GC[mbp1Codons[i]]
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}
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head(mbp1Codons)
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@ -238,7 +239,7 @@ for (i in 1:4) {
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dimnames(cCube)[[3]][k],
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sep = "",
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collapse = "")
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cCube[i, j, k] <- genCode[myCodon]
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cCube[i, j, k] <- GC[myCodon]
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}
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}
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}
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@ -249,6 +250,7 @@ cCube["T", "T", "T"] # phenylalanine
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cCube["T", "A", "G"] # stop (amber)
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# == 3.1 Print a Genetic code table ========================================
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@ -265,13 +267,15 @@ cCube["T", "A", "G"] # stop (amber)
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nuc <- c("T", "C", "A", "G")
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for (i in nuc) {
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for (k in nuc) {
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for (j in nuc) {
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cat(sprintf("%s%s%s: %s ", i, j, k, cCube[i, j, k]))
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# (calling variables f, s, t to indicate first, second, and third position ...)
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for (f in nuc) { # first varies in blocks
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for (t in nuc) { # third varies in columns
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for (s in nuc) { # second varies in rows
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cat(sprintf("%s%s%s: %s ", f, s, t, cCube[f, s, t]))
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}
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cat("\n")
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}
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cat("\n")
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}
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@ -335,7 +339,11 @@ for (i in nuc) {
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#
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#
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# Solution:
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table(table(Biostrings::GENETIC_CODE))
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( x <- table(table(Biostrings::GENETIC_CODE)) )
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# confirm
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sum(x * as.numeric(names(x)))
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# [END]
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