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hyginn 2020-10-13 20:27:56 +10:00
parent 307aad556e
commit 0541612e0b
1 changed files with 31 additions and 30 deletions
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scripts/ABC-dbUtilities.R
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@ -2,12 +2,13 @@
# #
# Purpose: Database utilities for ABC learning units. # Purpose: Database utilities for ABC learning units.
# #
# Version 2.1 # Version 2.2
# #
# Date: 2017-11 - 2020-10 # Date: 2017-11 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca) # Author: Boris Steipe (boris.steipe@utoronto.ca)
# #
# Versions: # Versions:
# 2.2 Bugfixes
# 2.1 Add JSON export functions # 2.1 Add JSON export functions
# 2.0 Test all JSON import and prevent addition of duplicates. This # 2.0 Test all JSON import and prevent addition of duplicates. This
# is necessary for import of data from the public page # is necessary for import of data from the public page
@ -33,26 +34,26 @@
#TOC> #TOC>
#TOC> Section Title Line #TOC> Section Title Line
#TOC> ------------------------------------------------------- #TOC> -------------------------------------------------------
#TOC> 1 INITIALISATIONS AND PARAMETERS 60 #TOC> 1 INITIALISATIONS AND PARAMETERS 61
#TOC> 2 PACKAGES 65 #TOC> 2 PACKAGES 66
#TOC> 3 FUNCTIONS 81 #TOC> 3 FUNCTIONS 82
#TOC> 3.01 dbSanitizeSequence() 84 #TOC> 3.01 dbSanitizeSequence() 85
#TOC> 3.02 dbConfirmUnique() 119 #TOC> 3.02 dbConfirmUnique() 120
#TOC> 3.03 dbInit() 137 #TOC> 3.03 dbInit() 138
#TOC> 3.04 dbAutoincrement() 177 #TOC> 3.04 dbAutoincrement() 178
#TOC> 3.05 dbAddProtein() 190 #TOC> 3.05 dbAddProtein() 191
#TOC> 3.06 dbAddFeature() 222 #TOC> 3.06 dbAddFeature() 224
#TOC> 3.07 dbAddTaxonomy() 253 #TOC> 3.07 dbAddTaxonomy() 255
#TOC> 3.08 dbAddAnnotation() 288 #TOC> 3.08 dbAddAnnotation() 290
#TOC> 3.09 dbFetchUniProtSeq() 335 #TOC> 3.09 dbFetchUniProtSeq() 337
#TOC> 3.10 dbFetchPrositeFeatures() 381 #TOC> 3.10 dbFetchPrositeFeatures() 383
#TOC> 3.11 node2text() 431 #TOC> 3.11 node2text() 433
#TOC> 3.12 dbFetchNCBItaxData() 443 #TOC> 3.12 dbFetchNCBItaxData() 445
#TOC> 3.13 UniProtIDmap() 482 #TOC> 3.13 UniProtIDmap() 484
#TOC> 3.14 dbProt2JSON() 521 #TOC> 3.14 dbProt2JSON() 523
#TOC> 3.15 dbSeq2JSON() 606 #TOC> 3.15 dbSeq2JSON() 608
#TOC> 3.16 dbRow2JSON() 636 #TOC> 3.16 dbRow2JSON() 637
#TOC> 4 TESTS 656 #TOC> 4 TESTS 657
#TOC> #TOC>
#TOC> ========================================================================== #TOC> ==========================================================================
@ -197,6 +198,7 @@ dbAddProtein <- function(db, jsonDF) {
# fromJSON() # fromJSON()
for (i in seq_len(nrow(jsonDF))) { for (i in seq_len(nrow(jsonDF))) {
isValid <- TRUE
if (jsonDF$name[i] %in% db$protein$name) { if (jsonDF$name[i] %in% db$protein$name) {
cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n", cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n",
i, jsonDF$name[i], i, jsonDF$name[i],
@ -237,7 +239,7 @@ dbAddFeature <- function(db, jsonDF) {
isValid <- FALSE isValid <- FALSE
} }
if (isVALID) { if (isValid) {
x <- data.frame(ID = dbAutoincrement(db$feature), x <- data.frame(ID = dbAutoincrement(db$feature),
name = jsonDF$name[i], name = jsonDF$name[i],
description = jsonDF$description[i], description = jsonDF$description[i],
@ -306,11 +308,11 @@ dbAddAnnotation <- function(db, jsonDF) {
sel <- db$annotation$proteinID == pID & sel <- db$annotation$proteinID == pID &
db$annotation$featureID == fID & db$annotation$featureID == fID &
db$annotation$start == as.integer(jsonDF$start[idx]) & db$annotation$start == as.integer(jsonDF$start[i]) &
db$annotation$end == as.integer(jsonDF$end[idx]) db$annotation$end == as.integer(jsonDF$end[i])
if (any(sel)) { if (any(sel)) {
cat(sprintf("Note: annotation No. %d in the input has %s%s%\n", cat(sprintf("Note: annotation No. %d in the input has %s%s\n",
i, i,
"the same protein name, feature name, start, and end ", "the same protein name, feature name, start, and end ",
"as one that already exists in the database. ", "as one that already exists in the database. ",
@ -630,7 +632,6 @@ dbSeq2JSON <- function(s, nIndents = 4, width = 70) {
out <- c(out, sprintf("%s]", ind)) out <- c(out, sprintf("%s]", ind))
return(paste0(out, collapse = "\n")) return(paste0(out, collapse = "\n"))
} }
cat(dbSeq2JSON(myDB$protein$sequence[1]))
# == 3.16 dbRow2JSON() ===================================================== # == 3.16 dbRow2JSON() =====================================================