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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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@ -2,17 +2,18 @@
# #
# 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:
# 2.1 Add JSON export functions # 2.2 Bugfixes
# 2.0 Test all JSON import and prevent addition of duplicates. This # 2.1 Add JSON export functions
# 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
# 1.1 2020 Updates # 1.1 2020 Updates
# 1.0 Live version 2017 # 1.0 Live version 2017
# #
# Notes: # Notes:
# There are no functions to modify or delete entries. To do either, # There are no functions to modify or delete entries. To do either,
@ -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() =====================================================