Mercurial > repos > prog > lcmsmatching

annotate MirbaseConn.R @ 5:18254e8d1b72 draft

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planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit 947b8707b06176a4801de64a71c8771617311ffb-dirty
author prog
date Thu, 16 Mar 2017 08:15:11 -0400
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1 #####################
45e985cd8e9e planemo upload for repository https://github.com/workflow4metabolomics/lcmsmatching.git commit d4048accde6bdfd5b3e14f5394902d38991854f8-dirty
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2 # CLASS DECLARATION #
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3 #####################
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5 MirbaseConn <- methods::setRefClass("MirbaseConn", contains = "RemotedbConn")
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7 ##########################
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8 # GET ENTRY CONTENT TYPE #
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9 ##########################
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11 MirbaseConn$methods( getEntryContentType = function() {
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12 return(BIODB.HTML)
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13 })
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15 #####################
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16 # GET ENTRY CONTENT #
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17 #####################
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19 MirbaseConn$methods( getEntryContent = function(ids) {
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21 # Initialize return values
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22 content <- rep(NA_character_, length(ids))
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24 # Request
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25 content <- vapply(ids, function(x) .self$.get.url(get.entry.url(BIODB.MIRBASE, x, content.type = BIODB.HTML)), FUN.VALUE = '')
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27 return(content)
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28 })
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30 ################
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31 # CREATE ENTRY #
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32 ################
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34 MirbaseConn$methods( createEntry = function(content, drop = TRUE) {
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35 return(createMirbaseEntryFromHtml(content, drop = drop))
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36 })
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38 ###################
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39 # FIND ACCESSIONS #
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40 ###################
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42 MirbaseConn$methods( findAccessions = function(name) {
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44 # Get HTML
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45 htmlstr <- .self$.get.url('http://www.mirbase.org/cgi-bin/query.pl', params = c(terms = name, submit = 'Search'))
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47 # Parse HTML
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48 xml <- htmlTreeParse(htmlstr, asText = TRUE, useInternalNodes = TRUE)
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50 # Get accession number
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51 acc <- unlist(xpathSApply(xml, "//a[starts-with(.,'MIMAT')]", xmlValue))
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53 return(acc)
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54 })