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bugfix in dbFetchPrositeFeatures(); add return of actual motif sequence; stylistic updates

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hyginn
2020-09-25 11:29:28 +10:00
parent 36140bc984
commit abb146f828
2 changed files with 42 additions and 36 deletions
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18
scripts/ABC-dbUtilities.R
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@@ -21,10 +21,10 @@
#TOC> 2.08 dbAddAnnotation() 215
#TOC> 2.09 dbFetchUniProtSeq() 243
#TOC> 2.10 dbFetchPrositeFeatures() 289
#TOC> 2.11 node2text() 333
#TOC> 2.12 dbFetchNCBItaxData() 345
#TOC> 2.13 UniProtIDmap() 384
#TOC> 3 TESTS 423
#TOC> 2.11 node2text() 339
#TOC> 2.12 dbFetchNCBItaxData() 351
#TOC> 2.13 UniProtIDmap() 390
#TOC> 3 TESTS 429
#TOC>
#TOC> ==========================================================================
@@ -297,6 +297,7 @@ dbFetchPrositeFeatures <- function(ID) {
# end num end of motif
# psID char PROSITE motif ID
# psName char PROSITE motif name
# psSeq char sequence annotated to the feature
# If the operation is not successful, a 0-length data frame is returned.
URL <- "https://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi"
@@ -313,7 +314,7 @@ dbFetchPrositeFeatures <- function(ID) {
lines <- unlist(strsplit(httr::content(response, "text"), "\\n"))
patt <- sprintf("\\|%s\\|", UniProtID)
patt <- sprintf("\\|%s\\|", ID)
lines <- lines[grep(patt, lines)]
for (line in lines) {
@@ -323,12 +324,17 @@ dbFetchPrositeFeatures <- function(ID) {
start = as.numeric(tokens[4]),
end = as.numeric(tokens[5]),
psID = tokens[6],
psName = tokens[7]))
psName = tokens[7],
psSeq = tokens[11]))
}
}
return(myFeatures)
}
if (FALSE) {
dbFetchPrositeFeatures("P33520") # RES1_SCHPO
}
# == 2.11 node2text() ======================================================
node2text <- function(doc, tag) {