Mercurial > repos > prog > lcmsmatching

annotate NcbigeneEntry.R @ 1:45e985cd8e9e draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
author prog
date Tue, 31 Jan 2017 05:27:24 -0500
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45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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1 #####################
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2 # CLASS DECLARATION #
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3 #####################
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5 NcbigeneEntry <- methods::setRefClass("NcbigeneEntry", contains = "BiodbEntry")
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6
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7 ###########
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8 # FACTORY #
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9 ###########
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11 createNcbigeneEntryFromXml <- function(contents, drop = TRUE) {
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12
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13 entries <- list()
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15 # Define xpath expressions
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16 xpath.expr <- character()
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17 xpath.expr[[BIODB.ACCESSION]] <- "//Gene-track_geneid"
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18 xpath.expr[[BIODB.KEGG.ID]] <- "/Dbtag_db[text()='KEGG']/..//Object-id_str"
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19 xpath.expr[[BIODB.UNIPROT.ID]] <- "//Gene-commentary_heading[text()='UniProtKB']/..//Dbtag_db[text()='UniProtKB/Swiss-Prot']/..//Object-id_str"
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20 xpath.expr[[BIODB.LOCATION]] <- "//Gene-ref_maploc"
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21 xpath.expr[[BIODB.PROTEIN.DESCRIPTION]] <- "//Gene-ref_desc"
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22 xpath.expr[[BIODB.SYMBOL]] <- "//Gene-ref_locus"
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23 xpath.expr[[BIODB.SYNONYMS]] <- "//Gene-ref_syn_E"
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25 for (content in contents) {
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26
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27 # Create instance
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28 entry <- NcbigeneEntry$new()
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29
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30 # Parse HTML
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31 xml <- XML::xmlInternalTreeParse(content, asText = TRUE)
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33 # An error occured
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34 if (length(XML::getNodeSet(xml, "//Error")) == 0 && length(XML::getNodeSet(xml, "//ERROR")) == 0) {
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35
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36 # Test generic xpath expressions
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37 for (field in names(xpath.expr)) {
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38 v <- XML::xpathSApply(xml, xpath.expr[[field]], XML::xmlValue)
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39 if (length(v) > 0) {
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40
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41 # Eliminate duplicates
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42 v <- v[ ! duplicated(v)]
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43
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44 # Set field
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45 entry$setField(field, v)
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46 }
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47 }
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49 # CCDS ID
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50 ccdsid <- .find.ccds.id(xml)
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51 if ( ! is.na(ccdsid))
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52 entry$setField(BIODB.NCBI.CCDS.ID, ccdsid)
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53 }
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54
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55 entries <- c(entries, entry)
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56 }
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57
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58 # Replace elements with no accession id by NULL
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59 entries <- lapply(entries, function(x) if (is.na(x$getField(BIODB.ACCESSION))) NULL else x)
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60
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61 # If the input was a single element, then output a single object
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62 if (drop && length(contents) == 1)
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63 entries <- entries[[1]]
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64
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65 return(entries)
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66
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67 # Get data
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68
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69 }
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71 ################
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72 # FIND CCDS ID #
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73 ################
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75 .find.ccds.id <- function(xml) {
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76
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77 # 1) Get all CCDS tags.
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78 ccds_elements <- XML::getNodeSet(xml, "//Dbtag_db[text()='CCDS']/..//Object-id_str")
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79
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80 # 2) If all CCDS are the same, go to point 4.
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81 ccds <- NA_character_
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82 for (e in ccds_elements) {
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83 current_ccds <- XML::xmlValue(e)
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84 if (is.na(ccds))
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85 ccds <- current_ccds
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86 else {
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87 if (current_ccds != ccds) {
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88 ccds <- NA_character_
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89 break
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90 }
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91 }
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92 }
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93
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94 # 3) There are several CCDS values, we need to find the best one (i.e.: the most current one).
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95 if (is.na(ccds)) {
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96 # For each CCDS, look for the parent Gene-commentary tag. Then look for the text content of the Gene-commentary_label which is situed under. Ignore CCDS that have no Gene-commentary_label associated. Choose the CCDS that has the smallest Gene-commentary_label in alphabetical order.
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97 version <- NA_character_
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98 for (e in ccds_elements) {
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99 versions <- XML::xpathSApply(e, "ancestor::Gene-commentary/Gene-commentary_label", XML::xmlValue)
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100 if (length(versions) < 1) next
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101 current_version <- versions[[length(versions)]]
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102 if (is.na(version) || current_version < version) {
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103 version <- current_version
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104 ccds <- XML::xmlValue(e)
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105 }
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106 }
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107 }
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108
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109 return(ccds)
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110 }