kozo-niのはてなダイアリー

2008-11-23

[] cytoscape で とりあえず KEGGのIDだけ付いてるネットワークアトリビュートを追加するスクリプト 23:32  cytoscape で とりあえず KEGGのIDだけ付いてるネットワークにアトリビュートを追加するスクリプトを含むブックマーク

$LOAD_PATH << 'gems/1.8/gems/bio-1.2.1/lib'
$LOAD_PATH << 'site_ruby/1.8'
$LOAD_PATH << 'site_ruby'
$LOAD_PATH << '1.8'
$LOAD_PATH << '1.8/java'
$LOAD_PATH << 'jruby'

require 'set'
require 'java'
require 'bio'

include_class 'java.util.ArrayList'
include_class 'cytoscape.Cytoscape'
include_class 'cytoscape.data.CyAttributes'
include_class 'cytoscape.CyNode'
include_class 'cytoscape.CyEdge'
include_class 'cytoscape.CyNetwork'

nodes = Cytoscape.getCyNodesList
attrs = Cytoscape.getNodeAttributes
serv = Bio::KEGG::API.new

cBuffer = ""
rBuffer = ""

cBgetResults = ""
rBgetResults = ""

canonicalHash = Hash.new

nodes.each{|node|
    keggId = attrs.getAttribute(node.getIdentifier, "canonicalName")
    if canonicalHash[keggId] then
        canonicalHash[keggId] << node.getIdentifier
    else
        canonicalHash[keggId] = [node.getIdentifier]
    end

    case keggId
    when /^R/
        rBuffer = rBuffer + keggId.gsub!("R", "rn:R") + " "
    when /^C/
        cBuffer = cBuffer + keggId.gsub!("C", "cpd:C") + " "
    end
}

rBgetResults = serv.bget(rBuffer.strip)
cBgetResults = serv.bget(cBuffer.strip)

cAnnotationList = cBgetResults.split("\n///\n")
rAnnotationList = rBgetResults.split("\n///\n")

cAnnotationList.each{|annotation|
    annt = Bio::KEGG::COMPOUND.new(annotation)
    canonicalHash[annt.entry_id].each{|nodeId|
        attrs.setAttribute(nodeId, "formula", annt.formula)
        attrs.setAttribute(nodeId, "enzymes", annt.enzymes.join(', '))
        attrs.setAttribute(nodeId, "mass", annt.mass)
        attrs.setAttribute(nodeId, "name", annt.name)
        attrs.setAttribute(nodeId, "pathways", annt.pathways.join(', '))
    }
}

rAnnotationList.each{|annotation|
    annt = Bio::KEGG::REACTION.new(annotation)
    canonicalHash[annt.entry_id].each{|nodeId|
        attrs.setAttribute(nodeId, "enzymes", annt.enzymes.join(', '))
        attrs.setAttribute(nodeId, "equation", annt.equation)
        attrs.setAttribute(nodeId, "pathways", annt.pathways.join(', '))
    }
}

p "ok."
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