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minor maintenance

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hyginn 2020-09-25 12:01:08 +10:00
parent abb146f828
commit 404fb05c79
1 changed files with 10 additions and 16 deletions
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RPR-eUtils_XML.R
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@ -1,20 +1,15 @@
# tocID <- "RPR-eUtils_and_XML.R"
#
# ---------------------------------------------------------------------------- #
# PATIENCE ... #
# Do not yet work wih this code. Updates in progress. Thank you. #
# boris.steipe@utoronto.ca #
# ---------------------------------------------------------------------------- #
#
# Purpose: A Bioinformatics Course:
# R code accompanying the RPR-Scripting_data_downloads unit.
#
# Version: 1.1
# Version: 1.2
#
# Date: 2017 10 05
# Date: 2017-10 - 2020-09
# Author: Boris Steipe (boris.steipe@utoronto.ca)
#
# Versions:
# 1.2 2020 Updates
# 1.1 Change from require() to requireNamespace(),
# use <package>::<function>() idiom throughout
# 1.0 First ABC units version
@ -47,7 +42,6 @@
# = 1 Working with NCBI eUtils ============================================
# To begin, we load the xml2 package that contains functions
# we need to receive and parse html data. NCBI's eUtils send information in
# XML format so we need to be able to parse XML.
@ -71,7 +65,7 @@ eUtilsBase <- "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
# Then we assemble an URL that will search for get the
# unique, NCBI internal identifier, the GI number,
# unique, NCBI internal identifier,
# for our refSeqID...
URL <- paste(eUtilsBase,
"esearch.fcgi?", # ...using the esearch program
@ -86,16 +80,16 @@ URL
# To fetch a response in R, we use the function read_xml()
# with our URL as its argument.
(myXML <- xml2::read_xml(URL))
( myXML <- xml2::read_xml(URL) )
# This is XML. We can take the response apart into
# its indvidual components with the as_list() function.
# its individual components with the as_list() function.
xml2::as_list(myXML)
# Note how the XML "tree" is represented as a list of
# lists of lists ...
# If we know exactly what elelement we are looking for,
# If we know exactly what element we are looking for,
# we can extract it from this structure:
xml2::as_list(myXML)[["eSearchResult"]][["IdList"]][["Id"]][[1]]
@ -104,7 +98,7 @@ xml2::as_list(myXML)[["eSearchResult"]][["IdList"]][["Id"]][[1]]
# and the NCBI changes things A LOT!
# Somewhat more robust is to specify the type of element
# we want - its the text contained in an <id>...</id>
# we want - its the text contained in an <Id>...</Id>
# element, and use the XPath XML parsing language to
# retrieve it.
@ -128,7 +122,7 @@ node2text <- function(doc, tag) {
# using node2text() ...
(GID <- node2text(myXML, "Id"))
# The GI is the pivot for all our data requests at the
# The GI is the pivot for data requests at the
# NCBI.
# Let's first get the associated data for this GI
@ -160,7 +154,7 @@ URL <- paste0(eUtilsBase,
# clicking on dbFetchNCBItaxData() in the Environment pane.
# Test:
dbFetchNCBItaxData("NP_010227")
dbFetchNCBItaxData("XP_001837394")
# [END]