#!/usr/bin/env ruby # # psortplot_html.rb - A KEGG API demo script. Generates a HTML file of # genes marked by PSORT II predictions onto a # KEGG/PATHWAY map. # # Usage: # # % ruby psortplot_html.rb # % cat sce00010_psort2.html # % ruby psortplot_html.rb path:eco00010 # % cat eco00010_psort2.html # # Copyright (C) 2005 Mitsuteru C. Nakao # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # $Id: psortplot_html.rb,v 1.1 2005/10/12 02:10:11 nakao Exp $ # require 'bio' class KEGG DBGET_BASEURI = 'http://kegg.com/dbget-bin' WWW_BGET_BASEURI = DBGET_BASEURI + '/www_bget' WWW_PATHWAY_BASEURI = DBGET_BASEURI + '/get_pathway' # path := path:sce00010 def self.link_pathway(path0) path, path = path0.split(':') org_name = path.scan(/(^\w{3})/).to_s mapno = path.sub(org_name, '') str = "#{path0}" end # ec_num := ec:1.2.3.4 def self.link_ec(ec_num) ec = ec_num.sub(/^ec:/, '') str = "#{ec_num}" return str end # gene := eco:b0002 def self.link_genes(gene) org_name, gene_name = gene.split(':') str = "#{gene}" return str end end class PSORT COLOR_Palette = { 'csk' => "#FF0000", # 'cytoskeletal' 'cyt' => "#FF8000", # 'cytoplasmic' 'nuc' => "#FFFF00", # 'nuclear' 'mit' => "#80FF00", # 'mitochondrial' 'ves' => "#00FF00", # 'vesicles of secretory system' 'end' => "#00FF80", # 'endoplasmic reticulum' 'gol' => "#00FFFF", # 'Golgi' 'vac' => "#0080FF", # 'vacuolar' 'pla' => "#0000FF", # 'plasma membrane' 'pox' => "#8000FF", # 'peroxisomal' 'exc' => "#FF00FF", # 'extracellular, including cell wall' '---' => "#FF0080" # 'other' } end keggapi = Bio::KEGG::API.new psort2serv = Bio::PSORT::PSORT2.imsut # Obtains a list of genes on specified pathway pathway = ARGV.shift || "path:sce00010" genes = keggapi.get_genes_by_pathway(pathway) scl = Hash.new # protein subcelluler localizations ec = Hash.new # EC numbers serial = 0 sync_default = $stdout.sync $stdout.sync = true genes.each do |gene| print "#{(serial += 1).to_s.rjust(genes.size.to_s.size)}\t#{gene}\t" # Obtains amino acid sequence from KEGG GENES entry aaseq = keggapi.get_aaseqs([gene]) # Predicts protein subcellualr localization result = psort2serv.exec(aaseq) scl[gene] = result.pred print "#{scl[gene]}\t" # Obtains the EC number from KEGG GENES entry ec[gene] = keggapi.get_enzymes_by_gene(gene) puts "#{ec[gene].inspect}" end $stdout.sync = sync_default fg_list = Array.new bg_list = Array.new genes.each do |gene| fg_list << "#FF0000" bg_list << PSORT::COLOR_Palette[scl[gene]] end # coloring KEGG pathway according to gene's localization url = keggapi.color_pathway_by_objects(pathway, genes, fg_list, bg_list) puts "#{url} downloaded." # remove "path:" prefix from pathway_id path_code = pathway.sub(/^path:/, '') # save the result image image_file = "#{path_code}_psort2.gif" begin keggapi.save_image(url, image_file) end # create html with a color palette html = < PSORT II prediction protein subcellular localization map of KEGG/PATHWAY (#{pathway})

PSORT II prediction protein subcellular localization map of KEGG/PATHWAY (#{KEGG.link_pathway(pathway)})

END # generate gene table with localization names = Bio::PSORT::PSORT2::SclNames multi_genes = Hash.new(0) ec.values.flatten.sort.uniq.each do |ec_num| ec.find_all {|x| x[1].include?(ec_num) }.each do |gene| gene = gene[0] loc = scl[gene] color = PSORT::COLOR_Palette[loc] name = names[loc] multi_genes[gene] += 1 html += < END end end html += <

Gene

Localization

#{multi_genes[gene]}

#{KEGG.link_ec(ec_num)}

#{KEGG.link_genes(gene)}

#{name}

END # generate color code table also PSORT::COLOR_Palette.sort.each do |code, color| html += < END end html += <

Code	Color
#{code}	#{names[code]}

END # save generated HTML file html_file = "#{path_code}_psort2.html" File.open(html_file, "w+") do |file| file.puts html end puts "Open #{html_file}"