Mercurial > repos > prog > lcmsmatching

comparison NcbiCcdsCompound.R @ 1:253d531a0193 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
comparison
equal deleted inserted replaced
0:e66bb061af06 1:253d531a0193
25 25
26 # Parse HTML 26 # Parse HTML
27 xml <- htmlTreeParse(html, asText = TRUE, useInternalNodes = TRUE) 27 xml <- htmlTreeParse(html, asText = TRUE, useInternalNodes = TRUE)
28 28
29 if (length(getNodeSet(xml, "//*[starts-with(.,'No results found for CCDS ID ')]")) == 0) { 29 if (length(getNodeSet(xml, "//*[starts-with(.,'No results found for CCDS ID ')]")) == 0) {
30 compound$setField(RBIODB.ACCESSION, xpathSApply(xml, "//input[@id='DATA']", xmlGetAttr, "value")) 30 compound$setField(BIODB.ACCESSION, xpathSApply(xml, "//input[@id='DATA']", xmlGetAttr, "value"))
31 compound$setField(RBIODB.SEQUENCE, xpathSApply(xml, "//b[starts-with(.,'Nucleotide Sequence')]/../tt", xmlValue)) 31 compound$setField(BIODB.SEQUENCE, xpathSApply(xml, "//b[starts-with(.,'Nucleotide Sequence')]/../tt", xmlValue))
32 } 32 }
33 33
34 compounds <- c(compounds, compound) 34 compounds <- c(compounds, compound)
35 } 35 }
36 36
37 # Replace elements with no accession id by NULL 37 # Replace elements with no accession id by NULL
38 compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x) 38 compounds <- lapply(compounds, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
39 39
40 # If the input was a single element, then output a single object 40 # If the input was a single element, then output a single object
41 if (drop && length(contents) == 1) 41 if (drop && length(contents) == 1)
42 compounds <- compounds[[1]] 42 compounds <- compounds[[1]]
43 43