Mercurial > repos > prog > lcmsmatching
diff NcbiCcdsCompound.R @ 1:253d531a0193 draft
planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 36c9d8099c20a1ae848f1337c16564335dd8fb2b
| author | prog |
|---|---|
| date | Sat, 03 Sep 2016 17:02:01 -0400 |
| parents | e66bb061af06 |
| children |
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--- a/NcbiCcdsCompound.R Tue Jul 12 12:02:37 2016 -0400 +++ b/NcbiCcdsCompound.R Sat Sep 03 17:02:01 2016 -0400 @@ -27,15 +27,15 @@ xml <- htmlTreeParse(html, asText = TRUE, useInternalNodes = TRUE) if (length(getNodeSet(xml, "//*[starts-with(.,'No results found for CCDS ID ')]")) == 0) { - compound$setField(RBIODB.ACCESSION, xpathSApply(xml, "//input[@id='DATA']", xmlGetAttr, "value")) - compound$setField(RBIODB.SEQUENCE, xpathSApply(xml, "//b[starts-with(.,'Nucleotide Sequence')]/../tt", xmlValue)) + compound$setField(BIODB.ACCESSION, xpathSApply(xml, "//input[@id='DATA']", xmlGetAttr, "value")) + compound$setField(BIODB.SEQUENCE, xpathSApply(xml, "//b[starts-with(.,'Nucleotide Sequence')]/../tt", xmlValue)) } compounds <- c(compounds, compound) } # Replace elements with no accession id by NULL - compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x) + compounds <- lapply(compounds, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x) # If the input was a single element, then output a single object if (drop && length(contents) == 1)