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comparison UniprotEntry.R @ 2:20d69a062da3 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8
author prog
date Thu, 02 Mar 2017 08:55:00 -0500
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1:253d531a0193 2:20d69a062da3
1 #####################
2 # CLASS DECLARATION #
3 #####################
4
5 UniprotEntry <- methods::setRefClass("UniprotEntry", contains = "BiodbEntry")
6
7 ###########
8 # FACTORY #
9 ###########
10
11 createUniprotEntryFromXml <- function(contents, drop = FALSE) {
12
13 # Set XML namespace
14 ns <- c(uniprot = "http://uniprot.org/uniprot")
15
16 entries <- list()
17
18 # Define xpath expressions
19 xpath.values <- character()
20 xpath.values[[BIODB.NAME]] <- "/uniprot:uniprot/uniprot:entry/uniprot:name"
21 xpath.values[[BIODB.GENE.SYMBOLS]] <- "//uniprot:gene/uniprot:name"
22 xpath.values[[BIODB.FULLNAMES]] <- "//uniprot:protein//uniprot:fullName"
23 xpath.values[[BIODB.SEQUENCE]] <- "//uniprot:entry/uniprot:sequence"
24 xpath.values[[BIODB.ACCESSION]] <- "//uniprot:accession[1]"
25 xpath.attr <- list()
26 xpath.attr[[BIODB.KEGG.ID]] <- list(path = "//uniprot:dbReference[@type='KEGG']", attr = 'id')
27 xpath.attr[[BIODB.NCBI.GENE.ID]] <- list(path = "//uniprot:dbReference[@type='GeneID']", attr = 'id')
28 xpath.attr[[BIODB.ENZYME.ID]] <- list(path = "//uniprot:dbReference[@type='EC']", attr = 'id')
29 xpath.attr[[BIODB.MASS]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'mass')
30 xpath.attr[[BIODB.LENGTH]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'length')
31
32 for (content in contents) {
33
34 # Create instance
35 entry <- UniprotEntry$new()
36
37 # If the entity doesn't exist (i.e.: no <id>.xml page), then it returns an HTML page
38 if ( ! grepl("^<!DOCTYPE html ", content, perl = TRUE)) {
39
40 # Parse XML
41 xml <- XML::xmlInternalTreeParse(content, asText = TRUE)
42
43 # Test value xpath
44 for (field in names(xpath.values)) {
45 v <- XML::xpathSApply(xml, xpath.values[[field]], XML::xmlValue, namespaces = ns)
46 if (length(v) > 0)
47 entry$setField(field, v)
48 }
49
50 # Test attribute xpath
51 for (field in names(xpath.attr)) {
52 v <- XML::xpathSApply(xml, xpath.attr[[field]]$path, XML::xmlGetAttr, xpath.attr[[field]]$attr, namespaces = ns)
53 if (length(v) > 0)
54 entry$setField(field, v)
55 }
56
57 # Remove new lines from sequence string
58 seq <- entry$getField(BIODB.SEQUENCE)
59 if ( ! is.na(seq))
60 entry$setField(BIODB.SEQUENCE, gsub("\\n", "", seq))
61 }
62
63 entries <- c(entries, entry)
64 }
65
66 # Replace elements with no accession id by NULL
67 entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
68
69 # If the input was a single element, then output a single object
70 if (drop && length(contents) == 1)
71 entries <- entries[[1]]
72
73 return(entries)
74 }