updates; vectorized dbFetchUniProtSeq()
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# tocID <- "RPR-UniProt_GET.R"
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#
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# ---------------------------------------------------------------------------- #
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# PATIENCE ... #
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# Do not yet work wih this code. Updates in progress. Thank you. #
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# boris.steipe@utoronto.ca #
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# ---------------------------------------------------------------------------- #
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the RPR-Scripting_data_downloads unit.
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#
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# Version: 1.1
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# Version: 1.2
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#
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# Date: 2017 10 - 2019 01
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# Date: 2017-10 - 2020-09
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.2 2020 Maintenance. Made dbFetchUniProtSeq() vector-safe and
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# added FASTA headers as attribute
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# 1.1 Change from require() to requireNamespace(),
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# use <package>::<function>() idiom throughout
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# 1.0 First ABC units version
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@ -34,13 +30,13 @@
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#TOC> ==========================================================================
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#TOC>
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#TOC>
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#TOC> Section Title Line
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#TOC> ----------------------------------------------------------
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#TOC> 1 UniProt files via GET 41
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#TOC> 1.1 Task - fetchUniProtSeq() function 103
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#TOC> 2 Task solutions 110
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#TOC>
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#TOC> 1 UniProt files via GET 43
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#TOC> 1.1 Task - fetchUniProtSeq() function 105
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#TOC> 2 Task solutions 118
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#TOC>
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#TOC> ==========================================================================
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@ -51,7 +47,7 @@
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# FASTA sequence from UniProt. All we need is to construct an URL with the
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# correct UniProt ID.
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# An interface between R scripts and We=b servers is provided by the httr
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# An interface between R scripts and Web servers is provided by the httr::
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# package. This sends and receives information via the http protocol, just like
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# a Web browser. Since this is a short and simple request, the GET verb is the
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# right tool:
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@ -108,21 +104,31 @@ httr::status_code(response)
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# == 1.1 Task - fetchUniProtSeq() function =================================
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# Task: write a function that takes as input a UniProt ID, fetches the
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# FASTA sequence, returns only the sequence if the operation is successful, or
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# a vector of length 0 if there is an error.
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# Task: write a function that
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# - takes as input a vector of UniProt IDs,
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# - fetches the FASTA sequence for each
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# - returns a vector of the same length as the input, where an element is:
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# - ... the sequence, if the query was successful
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# - ... NA if there was an error
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# - each element has the UniProt ID as the name()
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# - bonus: the output has an attribute "headers" that is a vector of the
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# FASTA headers ( cf. ?attr )
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# = 2 Task solutions ======================================================
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# I have placed such a function into the dbUtilities script: look it up by
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# clicking on dbFetchUniProtSeq() in the Environment pane.
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# Test:
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dbFetchUniProtSeq("P39678")
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# I have placed such a function - dbFetchUniProtSeq() - into
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# "./scripts/ABC-dbUtilities.R": look it up by clicking on dbFetchUniProtSeq()
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# in the Environment pane.
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# Test this:
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( x <- dbFetchUniProtSeq("P39678") )
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names(x)[1]
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attr(x, "headers")[1]
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x[1]
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cat(writeFASTA(data.frame(head = attr(x, "headers")[1], seq =x[1]),
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width = 40), sep = "\n")
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@ -20,11 +20,11 @@
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#TOC> 2.07 dbAddTaxonomy() 199
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#TOC> 2.08 dbAddAnnotation() 215
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#TOC> 2.09 dbFetchUniProtSeq() 243
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#TOC> 2.10 dbFetchPrositeFeatures() 267
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#TOC> 2.11 node2text() 311
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#TOC> 2.12 dbFetchNCBItaxData() 323
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#TOC> 2.13 UniProtIDmap() 362
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#TOC> 3 TESTS 401
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#TOC> 2.10 dbFetchPrositeFeatures() 289
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#TOC> 2.11 node2text() 333
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#TOC> 2.12 dbFetchNCBItaxData() 345
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#TOC> 2.13 UniProtIDmap() 384
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#TOC> 3 TESTS 423
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#TOC>
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#TOC> ==========================================================================
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@ -241,28 +241,50 @@ dbAddAnnotation <- function(db, jsonDF) {
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# == 2.09 dbFetchUniProtSeq() ==============================================
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dbFetchUniProtSeq <- function(ID) {
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dbFetchUniProtSeq <- function(IDs) {
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# Fetch a protein sequence from UniProt.
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# Parameters:
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# ID char a UniProt ID (accession number)
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# IDs char a vector of UniProt IDs (accession number)
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# Value:
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# char the sequence
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# If the operation is not successful, a 0-length string is returned
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# char a vector of the same length as ID. It contains
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# sequences where the retrieval was successful, NA where
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# it was not successful. The elements are named with
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# the ID, the header lines are set as attribute "header"
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URL <- sprintf("http://www.uniprot.org/uniprot/%s.fasta", ID)
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response <- httr::GET(URL)
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BASE <- "http://www.uniprot.org/uniprot/"
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mySeq <- character()
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if (httr::status_code(response) == 200) {
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x <- as.character(response)
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x <- strsplit(x, "\n")
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mySeq <- dbSanitizeSequence(x)
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sq <- character()
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hd <- character()
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for (i in seq_along(IDs)) {
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URL <- sprintf("%s%s.fasta", BASE, IDs[i])
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response <- httr::GET(URL)
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if (httr::status_code(response) == 200) {
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s <- as.character(response)
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s <- unlist(strsplit(s, "\n"))
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x <- dbSanitizeSequence(s)
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} else {
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s <- ""
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x <- NA
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}
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hd[i] <- s[1]
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sq[i] <- x
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}
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names(sq) <- IDs
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attr(sq, "headers") <- hd
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return(mySeq)
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return(sq)
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}
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if (FALSE) {
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inp <- c("P79073", "P0000000", "A0A1W2TKZ7")
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s <- dbFetchUniProtSeq(inp)
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s[1:3]
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str(s)
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attr(s, "headers")[1]
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}
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# == 2.10 dbFetchPrositeFeatures() =========================================
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dbFetchPrositeFeatures <- function(ID) {
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