bio 0.7.0

data/lib/bio/shell/plugin/codon.rb

@@ -0,0 +1,228 @@
+#
+# = bio/shell/plugin/codon.rb - plugin for the codon table
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: codon.rb,v 1.12 2005/12/19 02:34:24 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  class ColoredCodonTable
+
+    @@properties = {
+      :basic => %w( H K R ),
+      :polar => %w( S T Y Q N S ),
+      :acidic => %w( D E ),
+      :nonpolar => %w( F L I M V P A C W G ),
+      :stop => %w( * ),
+    }
+
+    def initialize(number, cuhash = nil)
+      @aacode = Bio::AminoAcid.names
+      @table  = Bio::CodonTable[number]
+      @number = number
+      @cuhash = cuhash
+      setup_colors
+      if Bio::Shell.config[:color]
+        generate_colored_text
+      else
+        generate_mono_text
+      end
+    end
+    attr_reader :table
+
+    def setup_colors
+      esc_seq = Bio::Shell.esc_seq
+
+      @colors = {
+        :text		=> esc_seq[:none],
+        :aa		=> esc_seq[:green],
+        :start		=> esc_seq[:red],
+        :stop		=> esc_seq[:red],
+        :basic		=> esc_seq[:cyan],
+        :polar		=> esc_seq[:blue],
+        :acidic		=> esc_seq[:magenta],
+        :nonpolar	=> esc_seq[:yellow],
+      }
+    end
+
+    def generate_mono_text
+      @table.each do |codon, aa|
+        if aa == '*'
+          code = "STOP"
+          aa = '' unless @cuhash
+        else
+          code = @aacode[aa]
+        end
+        if @cuhash
+          percent = @cuhash[codon].to_s.rjust(6)
+          eval("@#{codon} = '#{aa}#{percent}'")
+        else
+          eval("@#{codon} = ' #{code} #{aa} '")
+        end
+      end
+
+      @hydrophilic = [
+        @@properties[:basic].join(" "), "(basic),",
+        @@properties[:polar].join(" "), "(polar),",
+        @@properties[:acidic].join(" "), "(acidic)",
+      ].join(" ")
+      @hydrophobic = @@properties[:nonpolar].join(" ") + " (nonpolar)"
+    end
+
+    def generate_colored_text
+      @table.each do |codon, aa|
+        property, = @@properties.detect {|key, list| list.include?(aa)}
+
+        if aa == '*'
+          color_code = "#{@colors[:stop]}STOP"
+          if @cuhash
+            color_aa = "#{@colors[:stop]}#{aa}"
+          else
+            color_aa = ''
+          end
+        else
+          color_code = "#{@colors[property]}#{@aacode[aa]}"
+          if @table.start_codon?(codon)
+            if @cuhash
+              color_aa = "#{@colors[:aa]}#{aa}"
+            else
+              color_aa = "#{@colors[:start]}#{aa}"
+            end
+          else
+            if @cuhash
+              color_aa = "#{@colors[property]}#{aa}"
+            else
+              color_aa = "#{@colors[:aa]}#{aa}"
+            end
+          end
+        end
+
+        if @cuhash
+          percent = @cuhash[codon].to_s.rjust(6)
+          eval("@#{codon} = '#{color_aa}#{@colors[:text]}#{percent}'")
+        else
+          eval("@#{codon} = ' #{color_code} #{color_aa}#{@colors[:text]} '")
+        end
+      end
+
+      @hydrophilic = [
+        "#{@colors[:basic]}basic#{@colors[:text]},",
+        "#{@colors[:polar]}polar#{@colors[:text]},",
+        "#{@colors[:acidic]}acidic#{@colors[:text]}"
+      ].join(" ")
+      @hydrophobic = "#{@colors[:nonpolar]}nonpolar"
+    end
+
+    def output
+      header = <<-END
+        #
+        # = Codon table #{@number} : #{@table.definition}
+        #
+        #   hydrophilic: #{@hydrophilic}
+        #   hydrophobic: #{@hydrophobic}
+      END
+      table = <<-END
+        #
+        # *---------------------------------------------*
+        # |       |              2nd              |     |
+        # |  1st  |-------------------------------| 3rd |
+        # |       |  U    |  C    |  A    |  G    |     |
+        # |-------+-------+-------+-------+-------+-----|
+        # | U   U |#{@ttt}|#{@tct}|#{@tat}|#{@tgt}|  u  |
+        # | U   U |#{@ttc}|#{@tcc}|#{@tac}|#{@tgc}|  c  |
+        # | U   U |#{@tta}|#{@tca}|#{@taa}|#{@tga}|  a  |
+        # |  UUU  |#{@ttg}|#{@tcg}|#{@tag}|#{@tgg}|  g  |
+        # |-------+-------+-------+-------+-------+-----|
+        # |  CCCC |#{@ctt}|#{@cct}|#{@cat}|#{@cgt}|  u  |
+        # | C     |#{@ctc}|#{@ccc}|#{@cac}|#{@cgc}|  c  |
+        # | C     |#{@cta}|#{@cca}|#{@caa}|#{@cga}|  a  |
+        # |  CCCC |#{@ctg}|#{@ccg}|#{@cag}|#{@cgg}|  g  |
+        # |-------+-------+-------+-------+-------+-----|
+        # |   A   |#{@att}|#{@act}|#{@aat}|#{@agt}|  u  |
+        # |  A A  |#{@atc}|#{@acc}|#{@aac}|#{@agc}|  c  |
+        # | AAAAA |#{@ata}|#{@aca}|#{@aaa}|#{@aga}|  a  |
+        # | A   A |#{@atg}|#{@acg}|#{@aag}|#{@agg}|  g  |
+        # |-------+-------+-------+-------+-------+-----|
+        # |  GGGG |#{@gtt}|#{@gct}|#{@gat}|#{@ggt}|  u  |
+        # | G     |#{@gtc}|#{@gcc}|#{@gac}|#{@ggc}|  c  |
+        # | G GGG |#{@gta}|#{@gca}|#{@gaa}|#{@gga}|  a  |
+        # |  GG G |#{@gtg}|#{@gcg}|#{@gag}|#{@ggg}|  g  |
+        # *---------------------------------------------*
+        #
+      END
+      if @cuhash
+        text = table
+      else
+        text = header + table
+      end
+      if Bio::Shell.config[:color]
+        text.gsub(/^\s+#/, @colors[:text])
+      else
+        text.gsub(/^\s+#/, '')
+      end
+    end
+
+  end
+
+  private
+
+  def codontable(num = 1, codon_usage = nil)
+    cct = ColoredCodonTable.new(num, codon_usage)
+    if codon_usage
+      return cct
+    else
+      puts cct.output
+      return cct.table
+    end
+  end
+
+  def codontables
+    tables = Bio::CodonTable::DEFINITIONS
+    tables.sort.each do |i, definition|
+      puts "#{i}\t#{definition}"
+    end
+    return tables
+  end
+
+  def aminoacids
+    names = Bio::AminoAcid.names
+    names.sort.each do |aa, code|
+      if aa.length == 1
+        puts "#{aa}\t#{code}\t#{names[code]}"
+      end
+    end
+    return names
+  end
+
+  def nucleicacids
+    names = Bio::NucleicAcid.names
+    %w(a t g c u r y w s k m b v h d n).each do |base|
+      puts "#{base}\t#{names[base]}\t#{names[base.upcase]}"
+    end
+    return names
+  end
+
+end
+

data/lib/bio/shell/plugin/entry.rb

@@ -0,0 +1,85 @@
+#
+# = bio/shell/plugin/entry.rb - extract entry and sequence
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: entry.rb,v 1.4 2005/12/07 05:12:07 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  private
+
+  # Obtain a Bio::Sequence::NA (DNA) or a Bio::Sequence::AA (Amino Acid)
+  # sequence from
+  #   * String     -- "atgcatgc" or "MQKKP"
+  #   * IO         -- io = IO.popen("gzip -dc db.gz") (first entry only)
+  #   * "filename" -- "gbvrl.gbk" (first entry only)
+  #   * "db:entry" -- "embl:BUM"  (entry is retrieved by the ent method)
+  def seq(arg)
+    seq = ""
+    if arg.kind_of?(Bio::Sequence)
+      seq = arg
+    elsif arg.respond_to?(:gets) or File.exists?(arg)
+      ent = flatauto(arg)
+    elsif arg[/:/]
+      str = ent(arg)
+      ent = flatparse(str)
+    else
+      tmp = arg
+    end
+
+    if ent.respond_to?(:seq)
+      tmp = ent.seq
+    elsif ent.respond_to?(:naseq)
+      seq = ent.naseq
+    elsif ent.respond_to?(:aaseq)
+      seq = ent.aaseq
+    end
+
+    if tmp and tmp.is_a?(String) and not tmp.empty?
+      seq = Bio::Sequence.auto(tmp)
+    end
+    return seq
+  end
+
+  # Obtain a database entry from
+  #   * IO          -- IO object (first entry only)
+  #   * "filename"  -- local file (first entry only)
+  #   * "db:entry"  -- local bioflat, OBDA, KEGG API
+  def ent(arg)
+    entry = ""
+    db, entry_id = arg.to_s.strip.split(/:/)
+    if arg.respond_to?(:gets) or File.exists?(arg)
+      entry = flatfile(arg)
+    elsif Bio::Shell.find_flat_dir(db)
+      entry = flatsearch(db, entry_id)
+    elsif obdadbs.include?(db)
+      entry = obdaentry(db, entry_id)
+    else
+      entry = bget(arg)
+    end
+    return entry
+  end
+
+end

data/lib/bio/shell/plugin/flatfile.rb

@@ -0,0 +1,119 @@
+#
+# = bio/shell/plugin/flatfile.rb - plugin for flatfile database
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: flatfile.rb,v 1.11 2005/11/30 01:57:18 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  private
+
+  def flatfile(filename)
+    if block_given?
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.each do |entry|
+          yield flat.entry_raw
+        end
+      end
+    else
+      entry = ''
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.next_entry
+        entry = flat.entry_raw
+      end
+      return entry
+    end
+  end
+
+  def flatauto(filename)
+    if block_given?
+      Bio::FlatFile.auto(filename) do |flat|
+        flat.each do |entry|
+          yield entry
+        end
+      end
+    else
+      entry = ''
+      Bio::FlatFile.auto(filename) do |flat|
+        entry = flat.next_entry
+      end
+      return entry
+    end
+  end
+
+  def flatparse(entry)
+    if cls = Bio::FlatFile.autodetect(entry)
+      return cls.new(entry)
+    end
+  end
+
+  def flatfasta(fastafile, *flatfiles)
+    puts "Saving fasta file (#{fastafile}) ... "
+    File.open(fastafile, "w") do |fasta|
+      flatfiles.each do |flatfile|
+        puts "  converting -- #{flatfile}"
+        Bio::FlatFile.auto(flatfile) do |flat|
+          flat.each do |entry|
+            header = "#{entry.entry_id} #{entry.definition}"
+            fasta.puts entry.seq.to_fasta(header, 50)
+          end
+        end
+      end
+    end
+    puts "done"
+  end
+
+  def flatindex(dbname, *flatfiles)
+    dir = Bio::Shell.create_flat_dir(dbname)
+    begin
+      print "Creating BioFlat index (#{dir}) ... "
+      bdb = format = options = nil
+      Bio::FlatFileIndex.makeindex(bdb, dir, format, options, *flatfiles)
+      puts "done"
+    rescue
+      warn "Error: Failed to create index (#{dir}) : #{$!}"
+    end
+  end
+
+  def flatsearch(dbname, keyword)
+    dir = Bio::Shell.find_flat_dir(dbname)
+    unless dir
+      warn "Error: Failed to open database (#{dbname})"
+      return
+    end
+    entry = ''
+    Bio::FlatFileIndex.open(dir) do |db|
+      if results = db.include?(keyword)
+        results.each do |entry_id|
+          entry << db.search_primary(entry_id).to_s
+        end
+      else
+        warn "Error: No hits found in #{dbname} (#{keyword})"
+      end
+    end
+    return entry
+  end
+
+end

data/lib/bio/shell/plugin/keggapi.rb

@@ -0,0 +1,187 @@
+#
+# = bio/shell/plugin/keggapi.rb - plugin for KEGG API
+#
+# Copyright::	Copyright (C) 2005
+#		Toshiaki Katayama <k@bioruby.org>
+# License::	LGPL
+#
+# $Id: keggapi.rb,v 1.8 2005/12/18 15:47:33 k Exp $
+#
+#--
+#
+#  This library is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU Lesser General Public
+#  License as published by the Free Software Foundation; either
+#  version 2 of the License, or (at your option) any later version.
+#
+#  This library 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
+#  Lesser General Public License for more details.
+#
+#  You should have received a copy of the GNU Lesser General Public
+#  License along with this library; if not, write to the Free Software
+#  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA
+#
+#++
+#
+
+module Bio::Shell
+
+  module Private
+    def keggapi_definition2tab(list)
+      ary = []
+      list.each do |entry|
+        ary << "#{entry.entry_id}:\t#{entry.definition}"
+      end
+      return ary
+    end
+  end
+
+  private
+
+  def keggapi
+    @keggapi ||= Bio::KEGG::API.new  
+  end
+
+  # DBGET
+
+  def binfo(db = "all")
+    result = keggapi.binfo(db)
+    puts result
+    return result
+  end
+
+  def bfind(str)
+    result = keggapi.bfind(str)
+    return result
+  end
+
+  def bget(str)
+    result = keggapi.bget(str)
+    if block_given?
+      yield result
+    else
+      return result
+    end
+  end
+
+  def btit(str)
+    result = keggapi.btit(str)
+    return result
+  end
+
+  def bconv(str)
+    result = keggapi.bconv(str)
+    return result
+  end
+
+  # DATABASES
+
+  def keggdbs
+    list = keggapi.list_databases
+    result = Bio::Shell.keggapi_definition2tab(list).join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  def keggorgs
+    list = keggapi.list_organisms
+    result = Bio::Shell.keggapi_definition2tab(list).sort.join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  def keggpathways(org = "map")
+    list = keggapi.list_pathways(org)
+    result = Bio::Shell.keggapi_definition2tab(list).join("\n")
+    puts result
+    return list.map {|x| x.entry_id}
+  end
+
+  def kegggenomeseq(org)
+    result = ""
+    require 'net/ftp'
+    Net::FTP.open("ftp.genome.jp", "anonymous") do |ftp|
+      path = "/pub/kegg/genomes/#{org}"
+      list = ftp.nlst(path)
+      file = list.grep(/.*genome$/).shift
+      if file
+        open("ftp://ftp.genome.jp/#{file}") do |file|
+          result = file.read
+        end
+      end
+    end
+    return result
+  end
+
+end
+
+=begin
+
+== BioRuby extensions
+
+--- get_all_best_best_neighbors_by_gene(genes_id)
+--- get_all_best_neighbors_by_gene(genes_id)
+--- get_all_reverse_best_neighbors_by_gene(genes_id)
+--- get_all_paralogs_by_gene(genes_id)
+--- get_all_genes_by_motifs(motif_id_list)
+--- get_all_oc_members_by_gene(genes_id)
+--- get_all_pc_members_by_gene(genes_id)
+--- get_all_genes_by_organism(org)
+--- get_all_linkdb_by_entry(entry_id, db)
+--- save_image(url, filename = nil)
+--- get_entries(ary = [])
+--- get_aaseqs(ary = [])
+--- get_naseqs(ary = [])
+--- get_definitions(ary = [])
+
+== Original KEGG API methods
+
+--- get_linkdb_by_entry(entry_id, db, start, max_results)
+--- get_best_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_reverse_best_neighbors_by_gene(genes_id, start, max_results)
+--- get_paralogs_by_gene(genes_id, start, max_results)
+--- get_motifs_by_gene(genes_id, db)
+--- get_genes_by_motifs(motif_id_list, start, max_results)
+--- get_ko_by_gene(genes_id)
+--- get_ko_by_ko_class(ko_class_id)
+--- get_genes_by_ko_class(ko_class_id, org, start, max_results)
+--- get_genes_by_ko(ko_id, org)
+--- get_oc_members_by_gene(genes_id, start, max_results)
+--- get_pc_members_by_gene(genes_id, start, max_results)
+--- mark_pathway_by_objects(pathway_id, object_id_list)
+--- color_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+--- get_html_of_marked_pathway_by_objects(pathway_id, object_id_list)
+--- get_html_of_colored_pathway_by_objects(pathway_id, object_id_list, fg_color_list, bg_color_list)
+--- get_genes_by_pathway(pathway_id)
+--- get_enzymes_by_pathway(pathway_id)
+--- get_compounds_by_pathway(pathway_id)
+--- get_glycans_by_pathway(pathway_id)
+--- get_reactions_by_pathway(pathway_id)
+--- get_kos_by_pathway(pathway_id)
+--- get_pathways_by_genes(genes_id_list)
+--- get_pathways_by_enzymes(enzyme_id_list)
+--- get_pathways_by_compounds(compound_id_list)
+--- get_pathways_by_glycans(glycan_id_list)
+--- get_pathways_by_reactions(reaction_id_list)
+--- get_pathways_by_kos(ko_id_list, org)
+--- get_linked_pathways(pathway_id)
+--- get_genes_by_enzyme(enzyme_id, org)
+--- get_enzymes_by_gene(genes_id)
+--- get_enzymes_by_compound(compound_id)
+--- get_enzymes_by_glycan(glycan_id)
+--- get_enzymes_by_reaction(reaction_id)
+--- get_compounds_by_enzyme(enzyme_id)
+--- get_compounds_by_reaction(reaction_id)
+--- get_glycans_by_enzyme(enzyme_id)
+--- get_glycans_by_reaction(reaction_id)
+--- get_reactions_by_enzyme(enzyme_id)
+--- get_reactions_by_compound(compound_id)
+--- get_reactions_by_glycan(glycan_id)
+--- get_genes_by_organism(org, start, max_results)
+--- get_number_of_genes_by_organism(org)
+--- convert_mol_to_kcf(mol_text)
+
+=end