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2020 updates - deactivate for maintenance

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hyginn
2020-09-18 21:56:30 +10:00
parent 89bdd14d1c
commit 37ef655d47
42 changed files with 447 additions and 243 deletions
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2
scripts/ABC-createRefDB.R
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@@ -8,7 +8,7 @@
# http://steipe.biochemistry.utoronto.ca/abc/index.php/Reference_species_for_fungi
#
# For the data model, see
# https://docs.google.com/drawings/d/1uupNvz18_FYFwyyVPebTM0CUxcJCPDQuxuIJGpjWQWg
# https://docs.google.com/presentation/d/13vWaVcFpWEOGeSNhwmqugj2qTQuH1eZROgxWdHGEMr0
# For the schema, see dbInit() in ./scripts/ABC-dbUtilities.R
#
# ==============================================================================

82
scripts/ABC-dbUtilities.R
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@@ -1,12 +1,35 @@
# ABC-dbUtilities.R
# tocID <- "scripts/ABC-dbUtilities.R"
#
# database utilities for ABC learning units
#
# ==============================================================================
#
# ====== PACKAGES ==============================================================
#TOC> ==========================================================================
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------------------
#TOC> 1 PACKAGES 32
#TOC> 2 FUNCTIONS 50
#TOC> 2.01 dbSanitizeSequence() 53
#TOC> 2.02 dbConfirmUnique() 88
#TOC> 2.03 dbInit() 106
#TOC> 2.04 dbAutoincrement() 147
#TOC> 2.05 dbAddProtein() 160
#TOC> 2.06 dbAddFeature() 180
#TOC> 2.07 dbAddTaxonomy() 199
#TOC> 2.08 dbAddAnnotation() 215
#TOC> 2.09 dbFetchUniProtSeq() 243
#TOC> 2.10 dbFetchPrositeFeatures() 267
#TOC> 2.11 node2text() 311
#TOC> 2.12 dbFetchNCBItaxData() 323
#TOC> 2.13 UniProtIDmap() 362
#TOC> 3 TESTS 399
#TOC>
#TOC> ==========================================================================
# = 1 PACKAGES ============================================================
if (! requireNamespace("jsonlite", quietly = TRUE)) {
@@ -24,9 +47,10 @@ if (! requireNamespace("xml2", quietly = TRUE)) {
}
# ====== FUNCTIONS =============================================================
# = 2 FUNCTIONS ===========================================================
# == 2.01 dbSanitizeSequence() =============================================
dbSanitizeSequence <- function(s, unambiguous = TRUE) {
# Remove FASTA header lines, if any,
# flatten any structure that s has,
@@ -61,6 +85,7 @@ dbSanitizeSequence <- function(s, unambiguous = TRUE) {
}
# == 2.02 dbConfirmUnique() ================================================
dbConfirmUnique <- function(x) {
# x is a vector of logicals.
# returns x if x has exactly one TRUE element.
@@ -78,24 +103,27 @@ dbConfirmUnique <- function(x) {
}
# == 2.03 dbInit() =========================================================
dbInit <- function() {
# Return an empty instance of the protein database
# Open the link and study the schema:
# https://docs.google.com/presentation/d/13vWaVcFpWEOGeSNhwmqugj2qTQuH1eZROgxWdHGEMr0
db <- list()
db$version <- "1.0"
db$protein <- data.frame(
ID = numeric(),
name = character(),
RefSeqID = character(),
UniProtID = character(),
taxonomyID = numeric(),
sequence = character(),
stringsAsFactors = FALSE)
sequence = character())
db$taxonomy <- data.frame(
ID = numeric(),
species = character(),
stringsAsFactors = FALSE)
species = character())
db$annotation <- data.frame(
@@ -103,21 +131,20 @@ dbInit <- function() {
proteinID = numeric(),
featureID = numeric(),
start = numeric(),
end = numeric(),
stringsAsFactors = FALSE)
end = numeric())
db$feature <- data.frame(
ID = numeric(),
name = character(),
description = character(),
sourceDB = character(),
accession = character(),
stringsAsFactors = FALSE)
accession = character())
return(db)
}
# == 2.04 dbAutoincrement() ================================================
dbAutoincrement <- function(tb) {
# Return a unique integer that can be used as a primary key
# Value:
@@ -130,6 +157,7 @@ dbAutoincrement <- function(tb) {
}
# == 2.05 dbAddProtein() ===================================================
dbAddProtein <- function(db, jsonDF) {
# Add one or more protein entries to the database db.
# Parameters:
@@ -142,14 +170,14 @@ dbAddProtein <- function(db, jsonDF) {
RefSeqID = jsonDF$RefSeqID[i],
UniProtID = jsonDF$UniProtID[i],
taxonomyID = jsonDF$taxonomyID[i],
sequence = dbSanitizeSequence(jsonDF$sequence[i]),
stringsAsFactors = FALSE)
sequence = dbSanitizeSequence(jsonDF$sequence[i]))
db$protein <- rbind(db$protein, x)
}
return(db)
}
# == 2.06 dbAddFeature() ===================================================
dbAddFeature <- function(db, jsonDF) {
# Add one or more feature entries to the database db.
# Parameters:
@@ -161,14 +189,14 @@ dbAddFeature <- function(db, jsonDF) {
name = jsonDF$name[i],
description = jsonDF$description[i],
sourceDB = jsonDF$sourceDB[i],
accession = jsonDF$accession[i],
stringsAsFactors = FALSE)
accession = jsonDF$accession[i])
db$feature <- rbind(db$feature, x)
}
return(db)
}
# == 2.07 dbAddTaxonomy() ==================================================
dbAddTaxonomy <- function(db, jsonDF) {
# Add one or more taxonomy entries to the database db.
# Parameters:
@@ -178,13 +206,13 @@ dbAddTaxonomy <- function(db, jsonDF) {
for (i in seq_len(nrow(jsonDF))) {
x <- data.frame(
ID = jsonDF$ID[i],
species = jsonDF$species[i],
stringsAsFactors = FALSE)
species = jsonDF$species[i])
db$taxonomy <- rbind(db$taxonomy, x)
}
return(db)
}
# == 2.08 dbAddAnnotation() ================================================
dbAddAnnotation <- function(db, jsonDF) {
# Add one or more annotation entries to the database db.
# Parameters:
@@ -205,14 +233,14 @@ dbAddAnnotation <- function(db, jsonDF) {
proteinID = pID,
featureID = fID,
start = as.integer(jsonDF$start[i]),
end = as.integer(jsonDF$end[i]),
stringsAsFactors = FALSE)
end = as.integer(jsonDF$end[i]))
db$annotation <- rbind(db$annotation, x)
}
return(db)
}
# == 2.09 dbFetchUniProtSeq() ==============================================
dbFetchUniProtSeq <- function(ID) {
# Fetch a protein sequence from UniProt.
# Parameters:
@@ -236,6 +264,7 @@ dbFetchUniProtSeq <- function(ID) {
}
# == 2.10 dbFetchPrositeFeatures() =========================================
dbFetchPrositeFeatures <- function(ID) {
# Fetch feature annotations from ScanProsite.
# Parameters:
@@ -272,14 +301,14 @@ dbFetchPrositeFeatures <- function(ID) {
start = as.numeric(tokens[4]),
end = as.numeric(tokens[5]),
psID = tokens[6],
psName = tokens[7],
stringsAsFactors = FALSE))
psName = tokens[7]))
}
}
return(myFeatures)
}
# == 2.11 node2text() ======================================================
node2text <- function(doc, tag) {
# an extractor function for the contents of elements
# between given tags in an XML response.
@@ -291,6 +320,7 @@ node2text <- function(doc, tag) {
}
# == 2.12 dbFetchNCBItaxData() =============================================
dbFetchNCBItaxData <- function(ID) {
# Fetch feature taxID and Organism from the NCBI.
# Parameters:
@@ -329,6 +359,7 @@ dbFetchNCBItaxData <- function(ID) {
# == 2.13 UniProtIDmap() ===================================================
UniProtIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
# Use UniProt ID mapping service to map one or more IDs
# Parameters:
@@ -351,8 +382,7 @@ UniProtIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
if (httr::status_code(response) == 200) { # 200: oK
myMap <- read.delim(file = textConnection(httr::content(response)),
sep = "\t",
stringsAsFactors = FALSE)
sep = "\t")
myMap <- myMap[ , c(1,3)]
colnames(myMap) <- c("From", "To")
} else {
@@ -366,7 +396,7 @@ UniProtIDmap <- function (s, mapFrom = "P_REFSEQ_AC", mapTo = "ACC") {
}
# ====== TESTS =================================================================
# = 3 TESTS ===============================================================
if (FALSE) {
if (! requireNamespace("testthat", quietly = TRUE)) {

2
scripts/ABC-makeScCCnet.R
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@@ -1,4 +1,4 @@
# ABC-makeScCCnet.R
# tocID <- "scripts/ABC-makeScCCnet.R"
#
# Create a subnetwork of high-confidence yeast genes with a "mitotic cell cycle"
# GOSlim annotation.

2
scripts/ABC-writeALN.R
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@@ -1,4 +1,4 @@
# ABC-writeALN.R
# tocID <- "scripts/ABC-writeALN.R"
#
# ToDo: calculate consensus line
# append sequence numbers

4
scripts/ABC-writeMFA.R
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@@ -40,7 +40,7 @@ writeMFA <- function(ali,
if (is.na(blockWidth)) {
stop("PANIC: parameter \"blockWidth\" must be numeric.")
}
if (blockWidth < 1){
if (! blockWidth > 0){
stop("PANIC: parameter \"blockWidth\" must be greater than zero.")
}
@@ -105,7 +105,7 @@ writeMFA <- function(ali,
txt <- c(txt, "") # append an empty line for readability
}
writeLines(txt, con= myCon)
writeLines(txt, con = myCon)
}

31
scripts/BLAST.R
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@@ -357,20 +357,23 @@ parseBLASTalignment <- function(hit) {
# ==== TESTS ===================================================================
# define query:
# q <- paste("IYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHI", # Mbp1 APSES domain
# "LKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQ",
# "GTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASP",
# sep="")
# or ...
# q <- "NP_010227" # refseq ID
#
# test <- BLAST(q,
# nHits = 100,
# E = 0.001,
# rid = "",
# limits = "txid4751[ORGN]")
# length(test$hits)
if (FALSE) {
# define query:
q <- paste("IYSARYSGVDVYEFIHSTGSIMKRKKDDWVNATHI", # Mbp1 APSES domain
"LKAANFAKAKRTRILEKEVLKETHEKVQGGFGKYQ",
"GTWVPLNIAKQLAEKFSVYDQLKPLFDFTQTDGSASP",
sep="")
# or ...
q <- "NP_010227" # refseq ID
test <- BLAST(q,
nHits = 100,
E = 0.001,
rid = "",
limits = "txid4751[ORGN]")
str(test)
length(test$hits)
}
# [END]