Line termination change and old code.
This commit is contained in:
@@ -1,21 +1,21 @@
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# .myProfile.R
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# This contains information which the course framework needs from time to time
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# to personalize assignments, validate submissions etc. Make sure that
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# the information correctly matches our official records.
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# myEmail char A string with your eMail address. Use your official
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# UofT eMail address.
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# myStudentNumber numeric Your UofT student number. Take care to have this
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# correct.
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#
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# NOTE:
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# After you have updated this script, move the file to your "myScripts" folder.
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# Utility scripts will look for it on the path: "./myScripts/.myProfile.R"
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#
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# ==============================================================================
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# options(stringsAsFactors = FALSE)
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myEMail <- "yh.deng@mail.utoronto.ca" # e.g. "u.franklin@utoronto.ca"
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myStudentNumber <- 1005845285 # e.g. 1003141592
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MYSPE <- "Cutaneotrichosporon oleaginosum"
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# [END]
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# .myProfile.R
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# This contains information which the course framework needs from time to time
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# to personalize assignments, validate submissions etc. Make sure that
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# the information correctly matches our official records.
|
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# myEmail char A string with your eMail address. Use your official
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# UofT eMail address.
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# myStudentNumber numeric Your UofT student number. Take care to have this
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# correct.
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#
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# NOTE:
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# After you have updated this script, move the file to your "myScripts" folder.
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# Utility scripts will look for it on the path: "./myScripts/.myProfile.R"
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#
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# ==============================================================================
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# options(stringsAsFactors = FALSE)
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myEMail <- "yh.deng@mail.utoronto.ca" # e.g. "u.franklin@utoronto.ca"
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myStudentNumber <- 1005845285 # e.g. 1003141592
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MYSPE <- "Cutaneotrichosporon oleaginosum"
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# [END]
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@@ -1,54 +1,51 @@
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myFA <- readFASTA("data/RAB39B_HSa_coding.fa")
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myFA <- rbind(myFA, readFASTA("data/PTPN5_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/PTPN11_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/KRAS_HSa_coding.fa"))
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rownames(myFA)<-c("RAB39B", "PTPN5", "PTPN11", "KRAS") # Assign row names
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gen_mutations <- function(seq, N) {
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stats <- c()
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stats <- cbind(stats, c(0, 0, 0))
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rownames(stats) <- c("silent", "missense", "nonsense")
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colnames(stats) <- c("occurrences")
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# Actual function
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for (i in 1:217) {
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# select index for mutation
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working_seq <- Biostrings::DNAString(seq)
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aa_seq <- Biostrings::translate(working_seq, no.init.codon = TRUE)
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mut_action <- sample(c("ins", "del", "sub"), 1, TRUE)
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mut_seq <- Biostrings::DNAString(seq)
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if (mut_action == "sub") {
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mut_index <- sample(1:length(working_seq), 1, replace = TRUE)
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possible_mutations <- Biostrings::DNA_BASES
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possible_mutations <- possible_mutations[possible_mutations != as.character(unlist(working_seq[mut_index]))]
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mut_change <- sample(possible_mutations, 1, replace = TRUE)
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mut_seq <- Biostrings::replaceLetterAt(mut_seq, mut_index, mut_change)
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} else if (mut_action == "ins") {
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mut_index <- sample(1:length(working_seq) - 2, 1, replace = TRUE)
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possible_mutations <- Biostrings::DNA_BASES
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mut_seq <- Biostrings::DNAString(paste(substring(working_seq, 1, mut_index - 1), sample(possible_mutations, 1), substring(working_seq, mut_index), sep = ""))
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} else {
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mut_index <- sample(1:length(working_seq), 1, replace = TRUE)
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mut_seq <- mut_seq[-mut_index]
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}
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mut_seq <- Biostrings::DNAString(substring(mut_seq, 1, length(mut_seq) - (length(mut_seq) %% 3)))
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mut_aa <- Biostrings::translate(mut_seq, no.init.codon = TRUE)
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# Note: we need silent, nonsense, and missense
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mut_aa_stop <- match("*", Biostrings::as.matrix(mut_aa))
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aa_seq_stop <- match("*", Biostrings::as.matrix(aa_seq))
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if (!is.na(mut_aa_stop) & (is.na(aa_seq_stop) | mut_aa_stop < aa_seq_stop)) {
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stats["nonsense", "occurrences"] <- 1 + stats["nonsense", "occurrences"]
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} else if (mut_aa == aa_seq) {
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stats["silent", "occurrences"] <- 1 + stats["silent", "occurrences"]
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} else {
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stats["missense", "occurrences"] <- 1 + stats["missense", "occurrences"]
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}
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}
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return(stats)
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}
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N_test <- 1200
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gen_mutations("ATGATGATGATGATGATG", N_test)
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gen_mutations("CCCCCCCCCCCCCCCCCC", N_test)
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gen_mutations("TATTACTATTACTATTAC", N_test)
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gen_mutations("TGGTGGTGGTGGTGGTGGTGGTGG", N_test)
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gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGT", N_test)
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gen_mutations <- function(seq, N) {
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sealKey() # See: http://steipe.biochemistry.utoronto.ca/abc/index.php/BCH441_Code_submisson_instructions
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stats <- c()
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stats <- cbind(stats, c(0, 0, 0))
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rownames(stats) <- c("silent", "missense", "nonsense")
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colnames(stats) <- c("occurrences")
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# Actual function
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for (i in 1:N) {
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original_seq <- Biostrings::DNAString(seq)
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aa_seq <- Biostrings::translate(original_seq, no.init.codon = TRUE)
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mut_seq <- Biostrings::DNAString(seq)
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mut_index <- sample(1:length(original_seq), 1, replace = TRUE)
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possible_mutations <- Biostrings::DNA_BASES
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possible_mutations <- possible_mutations[possible_mutations != as.character(unlist(original_seq[mut_index]))]
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mut_seq <- Biostrings::replaceLetterAt(mut_seq, mut_index, sample(possible_mutations, 1, replace = TRUE))
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mut_aa <- Biostrings::translate(mut_seq, no.init.codon = TRUE)
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term_aa <- regexpr(pattern = "\\*", aa_seq)
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term_mut_aa <- as.integer(regexpr(pattern = "\\*", mut_aa))
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if ((term_aa == -1 && term_mut_aa != -1) || (term_mut_aa != -1 && term_mut_aa < term_aa)) {
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stats["nonsense", "occurrences"] <- 1 + stats["nonsense", "occurrences"]
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} else if (mut_aa == aa_seq) {
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stats["silent", "occurrences"] <- 1 + stats["silent", "occurrences"]
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} else {
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stats["missense", "occurrences"] <- 1 + stats["missense", "occurrences"]
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}
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}
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sealKey()
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return(stats)
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}
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gen_mutations("ATGATGATGATGATGATG", 1000)
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gen_mutations("CCCCCCCCCCCCCCCCCC", 500)
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gen_mutations("TATTACTATTACTATTAC", 500)
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gen_mutations("TGGTGGTGGTGGTGGTGGTGGTGG", 500)
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gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGT", 500)
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gen_mutations("TGTTGTTGTTGTTGTTGTTGTTGA", 500)
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myFA <- readFASTA("data/RAB39B_HSa_coding.fa")
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myFA <- rbind(myFA, readFASTA("data/PTPN5_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/PTPN11_HSa_coding.fa"))
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myFA <- rbind(myFA, readFASTA("data/KRAS_HSa_coding.fa"))
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rownames(myFA)<-c("RAB39B", "PTPN5", "PTPN11", "KRAS") # Assign row names
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gen_mutations(myFA["RAB39B", 2], 10000)
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gen_mutations(myFA["PTPN5", 2], 10000)
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gen_mutations(myFA["PTPN11", 2], 10000)
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gen_mutations(myFA["KRAS", 2], 10000)
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@@ -1,41 +1,41 @@
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# == 1.3 Task: submit for credit (part 1/2) ================================
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# == Submission - Code to add another philosopher to the datamodel:
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pID <- autoincrement(philDB$person)
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immanuelKant <- data.frame(id = pID,
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name = "Immanuel Kant",
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born = "1724",
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died = "1804",
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school = "Enlightenment Philosophy")
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philDB$person <- rbind(philDB$person, immanuelKant)
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bID = autoincrement(philDB$books)
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immanuelKantWork <- data.frame(id = bID,
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title = "Critique of Pure Reason",
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published = "1781")
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philDB$books <- rbind(philDB$books, immanuelKantWork)
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philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
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bID = autoincrement(philDB$books)
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immanuelKantWork <- data.frame(id = bID,
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title = "Critique of Judgement",
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published = "1790")
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philDB$books <- rbind(philDB$books, immanuelKantWork)
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philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
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# == Submission: Code to list the philosophical schools in alphabetical order as well as their respective books in alphabetical order.
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schools <- unique(philDB$person$school)
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schools <- sort(schools)
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for (s in schools) {
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cat(sprintf("%s\n", s))
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authors = which(philDB$person$school == s)
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for (author in authors) {
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works = which(philDB$works$personID == author)
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for (work in works) {
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bookId = which(philDB$books$id == philDB$works$bookID[work])
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cat(sprintf("\t%s - (%s)\n", philDB$books$title[bookId], philDB$books$published[bookId]))
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}
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}
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# == 1.3 Task: submit for credit (part 1/2) ================================
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# == Submission - Code to add another philosopher to the datamodel:
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pID <- autoincrement(philDB$person)
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immanuelKant <- data.frame(id = pID,
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name = "Immanuel Kant",
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born = "1724",
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died = "1804",
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school = "Enlightenment Philosophy")
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philDB$person <- rbind(philDB$person, immanuelKant)
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bID = autoincrement(philDB$books)
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immanuelKantWork <- data.frame(id = bID,
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title = "Critique of Pure Reason",
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published = "1781")
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philDB$books <- rbind(philDB$books, immanuelKantWork)
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philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
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bID = autoincrement(philDB$books)
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immanuelKantWork <- data.frame(id = bID,
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title = "Critique of Judgement",
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published = "1790")
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philDB$books <- rbind(philDB$books, immanuelKantWork)
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philDB$works <- rbind(philDB$works, data.frame(id = autoincrement(philDB$works), personID = pID, bookID = bID))
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# == Submission: Code to list the philosophical schools in alphabetical order as well as their respective books in alphabetical order.
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schools <- unique(philDB$person$school)
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schools <- sort(schools)
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for (s in schools) {
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cat(sprintf("%s\n", s))
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authors = which(philDB$person$school == s)
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for (author in authors) {
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works = which(philDB$works$personID == author)
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for (work in works) {
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bookId = which(philDB$books$id == philDB$works$bookID[work])
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cat(sprintf("\t%s - (%s)\n", philDB$books$title[bookId], philDB$books$published[bookId]))
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}
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}
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}
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@@ -1,4 +1,4 @@
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[{
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||||
"ID": 879819,
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"species": "Cutaneotrichosporon oleaginosum"}
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]
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[{
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||||
"ID": 879819,
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||||
"species": "Cutaneotrichosporon oleaginosum"}
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]
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@@ -1,19 +1,19 @@
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[
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||||
{ "name" : "MBP1_CUTOL",
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||||
"RefSeqID" : "XP_018278493.1",
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||||
"UniProtID" : "A0A0J0XLN0",
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"taxonomyID" : 879819,
|
||||
"sequence" : [
|
||||
"MGKKAAAAGDGGPNTIYKATYSGVPVFEFICRNVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQ",
|
||||
"KGEHEKVQGGYGKYQGTWVPIERGLALAKQYNVEDLLRPIIDFVPRESVSPPPAPKHAVAPPTKRNKEPK",
|
||||
"PKEGLVPIKSAGVLSGTGRHQTPDSVGEDVESEVMDDMSESQTPSPLNGTSLLPAVDERSIDGMDIDGFS",
|
||||
"MMNGGGHARKRSAAMMDDEDEYEQLKRARGNSAVHTPPPPGQSPRYGGMQHPLTQDEYNDIVLNYFVSEA",
|
||||
"TQIPAVMTNPPYNWDPNGIIDDDHHTALHWAAAMGRTRVIKLLLSAGARIFDKNNLDQTPLMRSVMFTNN",
|
||||
"YDLRKFPEVFELLHRSTLNIDKNNRTVFHHIANLALYKGKTHAARYYMEVILSRLADYPQELADVINFAD",
|
||||
"EDGETALTLAARARSKRIVKALLDHGADPKLRNRDHKSAEDYILEDERFRSSPDVMLNRTQPSAAPRNPT",
|
||||
"SLGAAVFSQGLPPQLYNSEAARLASGPHSSDILQQMQALARSFEAEKLNKERDVLEAKAMLTSIHTEVND",
|
||||
"AGRTLHNLGEQMKPLEAKQGELDGLVERLQSKLQKDLARGARKWKAADEGRENRWKNGDDPSQAGEDYSD",
|
||||
"LPELTAIPDNAEAEEERLRGEIEKMRARRGELVTRLVKAQTQTGTTDKMAQYRRLITAGCGGDINPGEID",
|
||||
"DIVGQLLDMLENEAQSGRPAPPPQAAPSWVTS"]
|
||||
}
|
||||
]
|
||||
[
|
||||
{ "name" : "MBP1_CUTOL",
|
||||
"RefSeqID" : "XP_018278493.1",
|
||||
"UniProtID" : "A0A0J0XLN0",
|
||||
"taxonomyID" : 879819,
|
||||
"sequence" : [
|
||||
"MGKKAAAAGDGGPNTIYKATYSGVPVFEFICRNVAVMRRRSDAYLNATQILKVAGFDKPQRTRVLEREVQ",
|
||||
"KGEHEKVQGGYGKYQGTWVPIERGLALAKQYNVEDLLRPIIDFVPRESVSPPPAPKHAVAPPTKRNKEPK",
|
||||
"PKEGLVPIKSAGVLSGTGRHQTPDSVGEDVESEVMDDMSESQTPSPLNGTSLLPAVDERSIDGMDIDGFS",
|
||||
"MMNGGGHARKRSAAMMDDEDEYEQLKRARGNSAVHTPPPPGQSPRYGGMQHPLTQDEYNDIVLNYFVSEA",
|
||||
"TQIPAVMTNPPYNWDPNGIIDDDHHTALHWAAAMGRTRVIKLLLSAGARIFDKNNLDQTPLMRSVMFTNN",
|
||||
"YDLRKFPEVFELLHRSTLNIDKNNRTVFHHIANLALYKGKTHAARYYMEVILSRLADYPQELADVINFAD",
|
||||
"EDGETALTLAARARSKRIVKALLDHGADPKLRNRDHKSAEDYILEDERFRSSPDVMLNRTQPSAAPRNPT",
|
||||
"SLGAAVFSQGLPPQLYNSEAARLASGPHSSDILQQMQALARSFEAEKLNKERDVLEAKAMLTSIHTEVND",
|
||||
"AGRTLHNLGEQMKPLEAKQGELDGLVERLQSKLQKDLARGARKWKAADEGRENRWKNGDDPSQAGEDYSD",
|
||||
"LPELTAIPDNAEAEEERLRGEIEKMRARRGELVTRLVKAQTQTGTTDKMAQYRRLITAGCGGDINPGEID",
|
||||
"DIVGQLLDMLENEAQSGRPAPPPQAAPSWVTS"]
|
||||
}
|
||||
]
|
||||
|
||||
@@ -1,8 +1,8 @@
|
||||
README - myScripts folder:
|
||||
==========================
|
||||
|
||||
The "myScripts" folder is a place to keep your personal files
|
||||
safe. No files will be submitted into this folder on the GitHub, master
|
||||
copy. Thefore everything you put into this folder is safe from being
|
||||
inadvertently overwritten by a file with the same name that would be
|
||||
downloaded in a GitHub "pull" request.
|
||||
README - myScripts folder:
|
||||
==========================
|
||||
|
||||
The "myScripts" folder is a place to keep your personal files
|
||||
safe. No files will be submitted into this folder on the GitHub, master
|
||||
copy. Thefore everything you put into this folder is safe from being
|
||||
inadvertently overwritten by a file with the same name that would be
|
||||
downloaded in a GitHub "pull" request.
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
source("./scripts/ABC-createRefDB.R")
|
||||
|
||||
myDB <- dbAddProtein(myDB, jsonlite::fromJSON("./myScripts/MBP1_CUTOL.json"))
|
||||
myDB <- dbAddTaxonomy(myDB, jsonlite::fromJSON("./myScripts/CUTOLtaxonomy.json"))
|
||||
source("./scripts/ABC-createRefDB.R")
|
||||
|
||||
myDB <- dbAddProtein(myDB, jsonlite::fromJSON("./myScripts/MBP1_CUTOL.json"))
|
||||
myDB <- dbAddTaxonomy(myDB, jsonlite::fromJSON("./myScripts/CUTOLtaxonomy.json"))
|
||||
|
||||
@@ -1,38 +1,38 @@
|
||||
# myScript.R
|
||||
#
|
||||
# --- As you work with this file, you can delete the instructions below --------
|
||||
# Write your notes and code experiments into this document. Save it
|
||||
# from time to time - however I recommend that you do not _commit_
|
||||
# your saved version.
|
||||
#
|
||||
# As long as you do not _commit_ this script to version control,
|
||||
# you can _pull_ updated versions of the entire project from GitHub
|
||||
# by using the RStudio version control interface. However, once
|
||||
# you _commit_ any file in your local version, RStudio will require
|
||||
# you to resolve conflicts before you can _pull_ updates.
|
||||
# --- As you work with this file, you can delete the instructions above --------
|
||||
#
|
||||
## Purpose: <...>
|
||||
#
|
||||
# Version: <...>
|
||||
#
|
||||
# Date: <...>
|
||||
# Author: <Name> (<namee@mail.utoronto.ca>)
|
||||
#
|
||||
# Versions:
|
||||
#
|
||||
# <number> <Features>
|
||||
#
|
||||
# TODO:
|
||||
# <...>
|
||||
#
|
||||
# ====================================================================
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
# [END]
|
||||
|
||||
# myScript.R
|
||||
#
|
||||
# --- As you work with this file, you can delete the instructions below --------
|
||||
# Write your notes and code experiments into this document. Save it
|
||||
# from time to time - however I recommend that you do not _commit_
|
||||
# your saved version.
|
||||
#
|
||||
# As long as you do not _commit_ this script to version control,
|
||||
# you can _pull_ updated versions of the entire project from GitHub
|
||||
# by using the RStudio version control interface. However, once
|
||||
# you _commit_ any file in your local version, RStudio will require
|
||||
# you to resolve conflicts before you can _pull_ updates.
|
||||
# --- As you work with this file, you can delete the instructions above --------
|
||||
#
|
||||
## Purpose: <...>
|
||||
#
|
||||
# Version: <...>
|
||||
#
|
||||
# Date: <...>
|
||||
# Author: <Name> (<namee@mail.utoronto.ca>)
|
||||
#
|
||||
# Versions:
|
||||
#
|
||||
# <number> <Features>
|
||||
#
|
||||
# TODO:
|
||||
# <...>
|
||||
#
|
||||
# ====================================================================
|
||||
|
||||
|
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# [END]
|
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|
||||
|
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Reference in New Issue
Block a user