Mercurial > repos > prog > lcmsmatching

annotate MirbaseCompound.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('MirbaseCompound')) { # 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')
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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5 #####################
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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6 # CLASS DECLARATION #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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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 MirbaseCompound <- setRefClass("MirbaseCompound", contains = "BiodbEntry")
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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11 ###########
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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12 # FACTORY #
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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13 ###########
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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15 createMirbaseCompoundFromHtml <- function(contents, drop = TRUE) {
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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17 library(XML)
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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19 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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21 # Define fields regex
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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22 xpath.expr <- character()
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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23 xpath.expr[[RBIODB.ACCESSION]] <- "//td[text()='Accession number']/../td[2]"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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24 xpath.expr[[RBIODB.NAME]] <- "//td[text()='ID']/../td[2]"
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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25 xpath.expr[[RBIODB.SEQUENCE]] <- "//td[text()='Sequence']/..//pre"
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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27 for (html in contents) {
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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29 # Create instance
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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30 compound <- ChebiCompound$new()
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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32 # Parse HTML
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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33 xml <- htmlTreeParse(html, asText = TRUE, useInternalNodes = TRUE)
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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35 # Test generic xpath expressions
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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36 for (field in names(xpath.expr)) {
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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37 v <- xpathSApply(xml, xpath.expr[[field]], xmlValue)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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38 if (length(v) > 0)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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39 compound$setField(field, v)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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40 }
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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42 compounds <- c(compounds, compound)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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43 }
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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45 # Replace elements with no accession id by NULL
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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46 compounds <- lapply(compounds, function(x) if (is.na(x$getField(RBIODB.ACCESSION))) NULL else x)
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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48 # If the input was a single element, then output a single object
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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49 if (drop && length(contents) == 1)
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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50 compounds <- compounds[[1]]
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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52 return(compounds)
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53 }
3afe41d3e9e7 planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit bb4d3e23d99828bfee16d31d794c49a17313ec2f
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54 }