Mercurial > repos > prog > lcmsmatching

annotate UniProtCompound.R @ 0:3afe41d3e9e7 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
author prog
date Mon, 11 Jul 2016 09:12:03 -0400
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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1 if ( ! exists('UniprotCompound')) { # Do not load again if already loaded
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3 source('BiodbEntry.R')
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5 #####################
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6 # CLASS DECLARATION #
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7 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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9 UniprotCompound <- setRefClass("UniprotCompound", contains = "BiodbEntry")
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11 ###########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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12 # FACTORY #
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13 ###########
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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15 createUniprotCompoundFromXml <- function(contents, drop = FALSE) {
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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17 library(XML)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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19 # Set XML namespace
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20 ns <- c(uniprot = "http://uniprot.org/uniprot")
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22 compounds <- list()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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24 # Define xpath expressions
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25 xpath.values <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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26 xpath.values[[RBIODB.NAME]] <- "/uniprot:uniprot/uniprot:compound/uniprot:name"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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27 xpath.values[[RBIODB.GENE.SYMBOLS]] <- "//uniprot:gene/uniprot:name"
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28 xpath.values[[RBIODB.FULLNAMES]] <- "//uniprot:protein//uniprot:fullName"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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29 xpath.values[[RBIODB.SEQUENCE]] <- "//uniprot:entry/uniprot:sequence"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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30 xpath.values[[RBIODB.ACCESSION]] <- "//uniprot:accession[1]"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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31 xpath.attr <- list()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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32 xpath.attr[[RBIODB.KEGG.ID]] <- list(path = "//uniprot:dbReference[@type='KEGG']", attr = 'id')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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33 xpath.attr[[RBIODB.NCBI.GENE.ID]] <- list(path = "//uniprot:dbReference[@type='GeneID']", attr = 'id')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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34 xpath.attr[[RBIODB.ENZYME.ID]] <- list(path = "//uniprot:dbReference[@type='EC']", attr = 'id')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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35 xpath.attr[[RBIODB.MASS]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'mass')
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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36 xpath.attr[[RBIODB.LENGTH]] <- list(path = "//uniprot:entry/uniprot:sequence", attr = 'length')
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38 for (content in contents) {
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3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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40 # Create instance
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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41 compound <- HmdbCompound$new()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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43 # If the entity doesn't exist (i.e.: no <id>.xml page), then it returns an HTML page
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44 if ( ! grepl("^<!DOCTYPE html ", content, perl = TRUE)) {
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46 # Parse XML
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47 xml <- xmlInternalTreeParse(content, asText = TRUE)
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49 # Test value xpath
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50 for (field in names(xpath.values)) {
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51 v <- xpathSApply(xml, xpath.values[[field]], xmlValue, namespaces = ns)
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52 if (length(v) > 0)
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53 compound$setField(field, v)
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54 }
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56 # Test attribute xpath
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57 for (field in names(xpath.attr)) {
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58 v <- xpathSApply(xml, xpath.attr[[field]]$path, xmlGetAttr, xpath.attr[[field]]$attr, namespaces = ns)
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59 if (length(v) > 0)
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60 compound$setField(field, v)
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61 }
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63 # Remove new lines from sequence string
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64 seq <- compound$getField(RBIODB.SEQUENCE)
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65 if ( ! is.na(seq))
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66 compound$setField(RBIODB.SEQUENCE, gsub("\\n", "", seq))
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67 }
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69 compounds <- c(compounds, compound)
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70 }
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72 # Replace elements with no accession id by NULL
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73 compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
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75 # If the input was a single element, then output a single object
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76 if (drop && length(contents) == 1)
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77 compounds <- compounds[[1]]
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79 return(compounds)
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80 }
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81 }