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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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53
scripts/ABC-dbUtilities.R
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@ -2,12 +2,13 @@
#
# Purpose: Database utilities for ABC learning units.
#
# Version 2.1
# Version 2.2
#
# Date: 2017-11 - 2020-10
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 2.2 Bugfixes
# 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
@ -33,26 +34,26 @@
#TOC>
#TOC> Section Title Line
#TOC> -------------------------------------------------------
#TOC> 1 INITIALISATIONS AND PARAMETERS 60
#TOC> 2 PACKAGES 65
#TOC> 3 FUNCTIONS 81
#TOC> 3.01 dbSanitizeSequence() 84
#TOC> 3.02 dbConfirmUnique() 119
#TOC> 3.03 dbInit() 137
#TOC> 3.04 dbAutoincrement() 177
#TOC> 3.05 dbAddProtein() 190
#TOC> 3.06 dbAddFeature() 222
#TOC> 3.07 dbAddTaxonomy() 253
#TOC> 3.08 dbAddAnnotation() 288
#TOC> 3.09 dbFetchUniProtSeq() 335
#TOC> 3.10 dbFetchPrositeFeatures() 381
#TOC> 3.11 node2text() 431
#TOC> 3.12 dbFetchNCBItaxData() 443
#TOC> 3.13 UniProtIDmap() 482
#TOC> 3.14 dbProt2JSON() 521
#TOC> 3.15 dbSeq2JSON() 606
#TOC> 3.16 dbRow2JSON() 636
#TOC> 4 TESTS 656
#TOC> 1 INITIALISATIONS AND PARAMETERS 61
#TOC> 2 PACKAGES 66
#TOC> 3 FUNCTIONS 82
#TOC> 3.01 dbSanitizeSequence() 85
#TOC> 3.02 dbConfirmUnique() 120
#TOC> 3.03 dbInit() 138
#TOC> 3.04 dbAutoincrement() 178
#TOC> 3.05 dbAddProtein() 191
#TOC> 3.06 dbAddFeature() 224
#TOC> 3.07 dbAddTaxonomy() 255
#TOC> 3.08 dbAddAnnotation() 290
#TOC> 3.09 dbFetchUniProtSeq() 337
#TOC> 3.10 dbFetchPrositeFeatures() 383
#TOC> 3.11 node2text() 433
#TOC> 3.12 dbFetchNCBItaxData() 445
#TOC> 3.13 UniProtIDmap() 484
#TOC> 3.14 dbProt2JSON() 523
#TOC> 3.15 dbSeq2JSON() 608
#TOC> 3.16 dbRow2JSON() 637
#TOC> 4 TESTS 657
#TOC>
#TOC> ==========================================================================
@ -197,6 +198,7 @@ dbAddProtein <- function(db, jsonDF) {
# fromJSON()
for (i in seq_len(nrow(jsonDF))) {
isValid <- TRUE
if (jsonDF$name[i] %in% db$protein$name) {
cat(sprintf("Note: Protein No. %d in the input is \"%s\", but %s.\n",
i, jsonDF$name[i],
@ -237,7 +239,7 @@ dbAddFeature <- function(db, jsonDF) {
isValid <- FALSE
}
if (isVALID) {
if (isValid) {
x <- data.frame(ID = dbAutoincrement(db$feature),
name = jsonDF$name[i],
description = jsonDF$description[i],
@ -306,11 +308,11 @@ dbAddAnnotation <- function(db, jsonDF) {
sel <- db$annotation$proteinID == pID &
db$annotation$featureID == fID &
db$annotation$start == as.integer(jsonDF$start[idx]) &
db$annotation$end == as.integer(jsonDF$end[idx])
db$annotation$start == as.integer(jsonDF$start[i]) &
db$annotation$end == as.integer(jsonDF$end[i])
if (any(sel)) {
cat(sprintf("Note: annotation No. %d in the input has %s%s%\n",
cat(sprintf("Note: annotation No. %d in the input has %s%s\n",
i,
"the same protein name, feature name, start, and end ",
"as one that already exists in the database. ",
@ -630,7 +632,6 @@ dbSeq2JSON <- function(s, nIndents = 4, width = 70) {
out <- c(out, sprintf("%s]", ind))
return(paste0(out, collapse = "\n"))
}
cat(dbSeq2JSON(myDB$protein$sequence[1]))
# == 3.16 dbRow2JSON() =====================================================