161 lines
5.0 KiB
R
161 lines
5.0 KiB
R
# tocID <- "RPR-eUtils_and_XML.R"
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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: 1.2
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#
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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 Updates
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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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# 0.1 First code copied from 2016 material.
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#
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#
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# TODO:
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#
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#
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# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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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 Working with NCBI eUtils 41
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#TOC> 1.1 Task - fetchNCBItaxData() function 144
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#TOC> 2 Task solutions 151
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#TOC>
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#TOC> ==========================================================================
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# = 1 Working with NCBI eUtils ============================================
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# To begin, we load the xml2 package that contains functions
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# we need to receive and parse html data. NCBI's eUtils send information in
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# XML format so we need to be able to parse XML.
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if (! requireNamespace("xml2", quietly=TRUE)) {
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install.packages("xml2")
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}
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# Package information:
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# library(help = xml2) # basic information
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# browseVignettes("xml2") # available vignettes
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# data(package = "xml2") # available datasets
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# We will walk through the process with the refSeqID
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# of yeast Mbp1
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refSeqID <- "NP_010227"
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# First we build a query URL...
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eUtilsBase <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
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# Then we assemble an URL that will search for get the
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# unique, NCBI internal identifier,
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# for our refSeqID...
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URL <- paste(eUtilsBase,
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"esearch.fcgi?", # ...using the esearch program
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# that finds an entry in an
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# NCBI database
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"db=protein",
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"&term=", refSeqID,
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sep="")
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# Copy the URL and paste it into your browser to see
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# what the response should look like.
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URL
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# To fetch a response in R, we use the function read_xml()
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# with our URL as its argument.
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( myXML <- xml2::read_xml(URL) )
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# This is XML. We can take the response apart into
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# its individual components with the as_list() function.
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xml2::as_list(myXML)
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# Note how the XML "tree" is represented as a list of
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# lists of lists ...
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# If we know exactly what element we are looking for,
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# we can extract it from this structure:
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xml2::as_list(myXML)[["eSearchResult"]][["IdList"]][["Id"]][[1]]
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# But this is not very robust, it would break with the
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# slightest change that the NCBI makes to their data format -
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# and the NCBI changes things A LOT!
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# Somewhat more robust is to specify the type of element
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# we want - its the text contained in an <Id>...</Id>
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# element, and use the XPath XML parsing language to
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# retrieve it.
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xml2::xml_find_all(myXML, "//Id") # returns a "node set"
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xml2::xml_text(xml2::xml_find_all(myXML, "//Id")) # returns the contents
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# of the node set
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# We will need to do this more than once, so we write a function
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# for it...
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node2text <- function(doc, tag) {
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# an extractor function for the contents of elements
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# between given tags in an XML response.
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# Contents of all matching elements is returned in
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# a vector of strings.
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path <- paste0("//", tag)
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nodes <- xml2::xml_find_all(doc, path)
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return(xml2::xml_text(nodes))
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}
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# using node2text() ...
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(GID <- node2text(myXML, "Id"))
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# The GI is the pivot for data requests at the
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# NCBI.
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# Let's first get the associated data for this GI
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URL <- paste0(eUtilsBase,
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"esummary.fcgi?",
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"db=protein",
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"&id=",
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GID,
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"&version=2.0")
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(myXML <- xml2::read_xml(URL))
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(taxID <- node2text(myXML, "TaxId"))
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(organism <- node2text(myXML, "Organism"))
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# This forms the base of a function that gets taxonomy data
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# from an Entrez result. You can write this!
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# == 1.1 Task - fetchNCBItaxData() function ================================
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# Task: write a function that takes as input a RefSeq ID, fetches the taxonomy
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# information, returns a list with taxID and organism, if the operation is
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# successful, or a list of length 0 if there is an error.
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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 dbFetchNCBItaxData() in the Environment pane.
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# Test:
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dbFetchNCBItaxData("XP_001837394")
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# [END]
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