Issue #54: mapping check script - under development

cycle20 · Sep 26, 2022 · dd04759 · dd04759
1 parent ed45cc7
commit dd04759
Showing 1 changed file with 19 additions and 0 deletions.
diff --git a/R/uniprot_mapping_check.R b/R/uniprot_mapping_check.R
@@ -0,0 +1,19 @@
+library(rvest)
+library(xml2)
+library(glue)
+
+UNIPROT_API <- 'https://rest.uniprot.org/uniprotkb/{UniProtId}?format=xml'
+
+checkUniProt <- function(UniProtId, geneName) {
+  doc <- xml2::read_xml(glue::glue(UNIPROT_API))
+  xml2::xml_ns_strip(doc)
+  nodeset <- xml2::xml_find_all(doc, xpath = '/uniprot/entry/gene/name[@type="primary"]')
+  firstValue <- xml2::xml_text(nodeset[1])
+  if (length(nodeset) > 1 || geneName != firstValue) {
+    print(paste0(UniProtId, " length: ", length(nodeset)))
+#  } else {
+#    print(glue::glue('{UniProtId}: {geneName} ok'))
+  }
+}
+
+checkUniProt('Q6P093', 'AADACL2')