bio 1.5.2 → 1.6.0.pre.20181210

data/lib/bio/shell/object.rb

@@ -1,71 +0,0 @@
-#
-# = bio/shell/object.rb - Object extension for the BioRuby shell
-#
-# Copyright::   Copyright (C) 2006
-#               Nobuya Tanaka <t@chemruby.org>,
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: object.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-
-require 'pp'
-require 'cgi'
-require 'yaml'
-
-### Object extention
-
-class Object
-  # Couldn't work for Fixnum (Marshal)
-  attr_accessor :memo
-
-  def output(format = :yaml)
-    case format
-    when :yaml
-      self.to_yaml
-    when :html
-      format_html
-    when :inspect
-      format_pp
-    when :png
-      # *TODO*
-    when :svg
-      # *TODO*
-    when :graph
-      # *TODO* (Gruff, RSRuby etc.)
-    else
-      #self.inspect.to_s.fold(80)
-      self.to_s
-    end
-  end
-
-  private
-
-  def format_html
-    "<pre>#{CGI.escapeHTML(format_pp)}</pre>"
-  end
-
-  def format_pp
-    str = ""
-    PP.pp(self, str)
-    return str
-  end
-
-end
-
-class Hash
-
-  private
-
-  def format_html
-    html = ""
-    html += "<table>"
-    @data.each do |k, v|
-      html += "<tr><td>#{k}</td><td>#{v}</td></tr>"
-    end
-    html += "</table>"
-    return html
-  end
-
-end
-

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

@@ -1,42 +0,0 @@
-#
-# = bio/shell/plugin/blast.rb - plugin for BLAST services
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: blast.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-
-module Bio::Shell
-
-  private
-
-  # GenomeNet
-
-  def keggblast(query)
-    server = Bio::Blast.remote("blastp", "genes", "", "genomenet_tab")
-
-    if query[/^>/]
-      data = Bio::FastaFormat.new(query)
-      desc = data.definition
-      tmp = getseq(data.seq)
-    else
-      desc = "query"
-      tmp = getseq(query)
-    end
-    
-    if tmp.respond_to?(:translate)
-      aaseq = tmp.translate
-    else
-      aaseq = tmp
-    end
-
-    fasta = aaseq.to_fasta(desc, 60)
-    result = server.query(fasta)
-    puts server.output
-    return result
-  end
-
-end
-

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

@@ -1,218 +0,0 @@
-#
-# = bio/shell/plugin/codon.rb - plugin for the codon table
-#
-# Copyright::   Copyright (C) 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: codon.rb,v 1.16 2007/04/05 23:35:41 trevor Exp $
-#
-
-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
-      c = Bio::Shell.colors
-
-      @colors = {
-        :text		=> c[:none],
-        :aa		=> c[:green],
-        :start		=> c[:red],
-        :stop		=> c[:red],
-        :basic		=> c[:cyan],
-        :polar		=> c[:blue],
-        :acidic		=> c[:magenta],
-        :nonpolar	=> c[: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 == '*'
-          if @cuhash
-            color_code = "#{@colors[:stop]}STOP"
-            color_aa = "#{@colors[:stop]}#{aa}"
-          else
-            color_code = "#{@colors[:stop]}STP"
-            case codon
-            when 'tga'
-              color_aa = "#{@colors[:text]}U"
-            when 'tag'
-              color_aa = "#{@colors[:text]}O"
-            else
-              color_aa = "#{@colors[:text]}*"
-            end
-          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/das.rb

@@ -1,58 +0,0 @@
-#
-# = bio/shell/plugin/keggdas.rb - plugin for KEGG DAS
-#
-# Copyright::   Copyright (C) 2006
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: das.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-
-module Bio
-
-  class DAS
-    def list_sequences
-      result = ""
-      self.get_dsn.each do |dsn|
-        src = dsn.source_id
-        self.get_entry_points(src).each do |ep|
-          data = [src, ep.entry_id, ep.start.to_i, ep.stop.to_i, "# #{ep.description}"].join("\t") + "\n"
-          puts data
-          result += data
-        end
-      end
-      return result
-    end
-  end
-
-end
-
-module Bio::Shell
-
-  private
-
-  # http://www.biodas.org/
-  # http://www.dasregistry.org/
-
-  def das(url = nil)
-    if url
-      @das = Bio::DAS.new(url)
-    else
-      @das ||= keggdas
-    end
-  end
-
-  def keggdas(url = "http://das.hgc.jp/cgi-bin/")
-    das(url)
-  end
-
-  def ensembl(url = "http://das.ensembl.org/")
-    das(url)
-  end
-
-  def wormbase(url = "http://www.wormbase.org/db/")
-    das(url)
-  end
-
-end
-

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

@@ -1,23 +0,0 @@
-#
-# = bio/shell/plugin/emboss.rb - methods to use EMBOSS
-#
-# Copyright::   Copyright (C) 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-# $Id: emboss.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
-#
-
-module Bio::Shell
-
-  private
-
-  def seqret(usa)
-    Bio::EMBOSS.seqret(usa)
-  end
-
-  def entret(usa)
-    Bio::EMBOSS.entret(usa)
-  end
-
-end

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

@@ -1,137 +0,0 @@
-#
-# = bio/shell/plugin/entry.rb - extract entry and sequence
-#
-# Copyright::   Copyright (C) 2005
-#               Toshiaki Katayama <k@bioruby.org>
-# License::     The Ruby License
-#
-#
-
-module Bio::Shell
-
-  private
-
-  # Read a text file and collect the first word of each line in array
-  def readlist(filename)
-    list = []
-    File.open(filename).each do |line|
-      list << line[/^\S+/]
-    end
-    return list
-  end
-
-  # 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 getseq(arg)
-    seq = ""
-    if arg.kind_of?(Bio::Sequence)
-      seq = arg
-    elsif arg.respond_to?(:gets) or File.exist?(arg)
-      ent = flatauto(arg)
-    elsif arg[/:/]
-      ent = getobj(arg)
-    else
-      tmp = arg
-    end
-
-    if ent.respond_to?(:seq)
-      tmp = ent.seq
-    elsif ent.respond_to?(:naseq)
-      #seq = ent.naseq
-      tmp = ent.naseq
-    elsif ent.respond_to?(:aaseq)
-      #seq = ent.aaseq
-      tmp = ent.aaseq
-    end
-
-    if tmp and tmp.is_a?(String) and not tmp.empty?
-      #seq = Bio::Sequence.auto(tmp).seq
-      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, EMBOSS, KEGG API
-  def getent(arg)
-    entry = ""
-    db, entry_id = arg.to_s.strip.split(/\:/, 2)
-
-    # local file
-    if arg.respond_to?(:gets) or File.exist?(arg)
-      puts "Retrieving entry from file (#{arg})"
-      entry = flatfile(arg)
-
-    # BioFlat in ./.bioruby/bioflat/ or ~/.bioinformatics/.bioruby/bioflat/
-    elsif Bio::Shell.find_flat_dir(db)
-      puts "Retrieving entry from local BioFlat database (#{arg})"
-      entry = flatsearch(db, entry_id)
-
-    # OBDA in ~/.bioinformatics/seqdatabase.ini
-    elsif obdadbs.include?(db)
-      puts "Retrieving entry from OBDA (#{arg})"
-      entry = obdaentry(db, entry_id)
-
-    else
-      # EMBOSS USA in ~/.embossrc
-      begin
-        str = entret(arg)
-      rescue SystemCallError
-        str = ''
-      end
-      if $? and $?.exitstatus == 0 and str.length != 0
-        puts "Retrieving entry from EMBOSS (#{arg})"
-        entry = str
-
-      # via Internet
-      else
-        case db.to_s.downcase
-        when 'genbank', 'gb', 'nuccore', 'indsc'
-          # NCBI
-          puts "Retrieving entry from NCBI eUtils"
-          entry = efetch(entry_id)
-
-        when 'embl', 'emb', /\Aembl/, /\Auni/, 'sp', /\Aensembl/
-          # EBI
-          puts "Retrieving entry from EBI Dbfetch"
-          db = 'embl' if db == 'emb'
-          db = 'uniprotkb' if db == 'uniprot' or db == 'sp'
-          entry = biofetch(db, entry_id)
-
-        when 'ddbj', 'dbj', 'dad'
-          # TogoWS REST
-          puts "Retrieving entry from TogoWS"
-          db = 'ddbj' if db == 'dbj'
-          entry = togowsentry(db, entry_id)
-
-        else
-          togodblist = Bio::TogoWS::REST.entry_database_list rescue []
-          if togodblist.include?(db) then
-            # TogoWS REST
-            puts "Retrieving entry from TogoWS"
-            entry = togowsentry(db, entry_id)
-          else
-            # KEGG API at http://www.genome.jp/kegg/soap/
-            puts "Retrieving entry from KEGG API (#{arg})"
-            entry = bget(arg)
-          end
-        end
-      end
-    end
-
-    return entry
-  end
-
-  # Obtain a parsed object from sources that ent() supports.
-  def getobj(arg)
-    str = getent(arg)
-    flatparse(str)
-  end
-
-end