bugfix in dbFetchPrositeFeatures(); add return of actual motif sequence; stylistic updates
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@ -1,20 +1,15 @@
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# tocID <- "RPR-PROSITE_POST.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
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# 1.1 Change from require() to requireNamespace(),
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# use <package>::<function>() idiom throughout,
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# 1.0.1 Updates for slightly changed interfaces
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@ -35,13 +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 Constructing a POST command from a Web query 42
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#TOC> 1.1 Task - fetchPrositeFeatures() function 142
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#TOC> 2 Task solutions 150
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#TOC>
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#TOC> 1 Constructing a POST command from a Web query 43
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#TOC> 1.1 Task - fetchPrositeFeatures() function 148
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#TOC> 2 Task solutions 156
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#TOC>
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#TOC> ==========================================================================
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@ -59,9 +54,10 @@ if (! requireNamespace("httr", quietly = TRUE)) {
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# We have reverse engineered the Web form for a ScanProsite request, and can now
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# construct a POST request. The command is similar to GET(), but we need an
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# explicit request body: a list of key/value pairs
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# We have reverse engineered the Web form for a ScanProsite request, and can
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# construct a valid POST request from knowing the required field names. The POST
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# command is similar to GET(), but we need an explicit request body that
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# contains a list of key/value pairs
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UniProtID <- "P39678"
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@ -79,19 +75,24 @@ response <- httr::POST(URL,
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httr::status_code(response) # If this is not 200, something went wrong and it
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# makes no sense to continue. If this persists, ask
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# on the mailing list what to do.
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# on the Discussion Board what to do.
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# The text contents of the response is available with the
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# content() function:
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httr::content(response, "text")
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# ... should show you the same as the page contents that
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# you have seen in the browser. The date we need Now we need to extract
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# the data from the page: we need regular expressions, but
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# only simple ones. First, we strsplit() the response into
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# individual lines, since each of our data elements is on
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# its own line. We simply split on the "\\n" newline character.
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# ... should show you the same as the page contents that you have seen in the
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# browser. Now we need to extract the data from the page. For this simple
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# example we can get away with using regular expressions, but in general we need
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# a real XML parser to parse HTML. We'll cover that in a later unit. Here, we
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# strsplit() the response into individual lines, since each of our data elements
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# is on its own line, and then capture the contents. The way Prosite has
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# formatted their HTML we can simply split on the "\\n" newline character - but
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# they could write the same valid HTML without any newline-characters at all.
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# Understand that we are working with a bit of a "hack" here: exploting
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# empirical assumptions rather than a formal specification. But sometimes quick
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# and dirty is fine, because quick.
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lines <- unlist(strsplit(httr::content(response, "text"), "\\n"))
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head(lines)
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@ -105,10 +106,9 @@ patt <- sprintf("\\|%s\\|", UniProtID)
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# ... and select only the lines that match this
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# pattern:
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lines <- lines[grep(patt, lines)]
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lines
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( lines <- lines[grep(patt, lines)] )
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# ... captures the four lines of output.
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# ... captures the three lines of output.
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# Now we break the lines apart into tokens: this is another application of
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# strsplit(), but this time we split either on "pipe" characters, "|" OR on tabs
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@ -137,7 +137,7 @@ for (line in lines) {
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end = as.numeric(tokens[5]),
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psID = tokens[6],
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psName = tokens[7],
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stringsAsFactors = FALSE))
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psSeq = tokens[11]))
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}
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features
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@ -149,8 +149,8 @@ features
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# Task: write a function that takes as input a UniProt ID, fetches the
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# features it contains from ScanProsite and returns a list as given above, or
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# a list of length 0 if there is an error.
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# features it contains from ScanProsite and returns a data frame as given above, or
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# an empty data frame if there is an error.
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# = 2 Task solutions ======================================================
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@ -160,7 +160,7 @@ features
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# clicking on dbFetchPrositeFeatures() in the Environment pane.
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# Test:
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dbFetchPrositeFeatures("P39678")
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dbFetchPrositeFeatures("Q5KMQ9")
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@ -21,10 +21,10 @@
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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() 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> 2.11 node2text() 339
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#TOC> 2.12 dbFetchNCBItaxData() 351
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#TOC> 2.13 UniProtIDmap() 390
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#TOC> 3 TESTS 429
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#TOC>
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#TOC> ==========================================================================
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@ -297,6 +297,7 @@ dbFetchPrositeFeatures <- function(ID) {
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# end num end of motif
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# psID char PROSITE motif ID
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# psName char PROSITE motif name
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# psSeq char sequence annotated to the feature
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# If the operation is not successful, a 0-length data frame is returned.
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URL <- "https://prosite.expasy.org/cgi-bin/prosite/PSScan.cgi"
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@ -313,7 +314,7 @@ dbFetchPrositeFeatures <- function(ID) {
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lines <- unlist(strsplit(httr::content(response, "text"), "\\n"))
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patt <- sprintf("\\|%s\\|", UniProtID)
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patt <- sprintf("\\|%s\\|", ID)
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lines <- lines[grep(patt, lines)]
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for (line in lines) {
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@ -323,12 +324,17 @@ dbFetchPrositeFeatures <- function(ID) {
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start = as.numeric(tokens[4]),
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end = as.numeric(tokens[5]),
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psID = tokens[6],
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psName = tokens[7]))
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psName = tokens[7],
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psSeq = tokens[11]))
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}
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}
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return(myFeatures)
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}
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if (FALSE) {
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dbFetchPrositeFeatures("P33520") # RES1_SCHPO
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}
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# == 2.11 node2text() ======================================================
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node2text <- function(doc, tag) {
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