wwood-bioruby 1.2.11

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

@@ -0,0 +1,45 @@
+#
+# = bio/shell/plugin/obda.rb - plugin for OBDA
+#
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License 
+#
+# $Id: obda.rb,v 1.10 2007/04/05 23:45:11 trevor Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  def obda
+    @obda ||= Bio::Registry.new
+  end
+
+  def obdaentry(dbname, entry_id)
+    db = obda.get_database(dbname)
+    unless db
+      warn "Error: No such database (#{dbname})"
+      return
+    end
+    entry = db.get_by_id(entry_id)
+    if block_given?
+      yield entry
+    else
+      return entry
+    end
+  end
+
+  def obdadbs
+    result = obda.databases.map {|db| db.database}
+    return result
+  end
+
+  def biofetch(db, id, style = 'raw', format = 'default')
+    serv = Bio::Fetch.new("http://www.ebi.ac.uk/cgi-bin/dbfetch")
+    result = serv.fetch(db, id, style, format)
+    return result
+  end
+
+end
+

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

@@ -0,0 +1,56 @@
+#
+# = bio/shell/plugin/psort.rb - plugin for PSORT
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: psort.rb,v 1.3 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  def psort1(str)
+    seq = getseq(str)
+    if seq.is_a?(Bio::Sequence::NA)
+      seq = seq.translate
+    end
+
+    psort = Bio::PSORT::PSORT1.imsut
+    fasta = seq.to_fasta
+
+    results = psort.exec(fasta).final_result
+    results.each do |result|
+      puts "#{result["certainty"].to_f*100.0}\t#{result["prediction"]}"
+    end
+    return results.first["prediction"]
+  end
+
+  def psort2(str)
+    seq = getseq(str)
+    if seq.is_a?(Bio::Sequence::NA)
+      seq = seq.translate
+    end
+
+    psort = Bio::PSORT::PSORT2.imsut
+    fasta = seq.to_fasta
+
+    results = psort.exec(fasta).prob.sort_by{|x, y| y}.reverse
+    results.each do |loc, prob|
+      next if prob <= 0.0
+      puts "#{prob}\t#{Bio::PSORT::PSORT2::SclNames[loc]}"
+    end
+    return results.first.first
+  end
+
+  def psort2locations
+    names = Bio::PSORT::PSORT2::SclNames
+    names.sort.each do |loc, desc|
+      puts "#{loc}\t#{desc}"
+    end
+    return names
+  end
+end
+

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

@@ -0,0 +1,247 @@
+#
+# = bio/shell/plugin/seq.rb - plugin for biological sequence manipulations
+#
+# Copyright::   Copyright (C) 2005
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     The Ruby License
+#
+# $Id: seq.rb,v 1.21 2007/04/05 23:35:41 trevor Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  # Convert sequence to colored HTML string
+  def htmlseq(str)
+    if str.kind_of?(Bio::Sequence)
+      seq = str
+    else
+      seq = getseq(str)
+    end
+
+    if seq.is_a?(Bio::Sequence::AA)
+      scheme = Bio::ColorScheme::Taylor
+    else
+      scheme = Bio::ColorScheme::Nucleotide
+    end
+
+    html = %Q[<div style="font-family:monospace;">\n]
+    seq.fold(50).each_byte do |c|
+      case c.chr
+      when "\n"
+        html += "<br>\n"
+      else
+        color = scheme[c.chr]
+        html += %Q[<span style="background:\##{color};">#{c.chr}</span>\n]
+      end
+    end
+    html += "</div>\n"
+    return html
+  end
+
+
+  def sixtrans(str)
+    seq = getseq(str)
+    [ 1, 2, 3, -1, -2, -3 ].each do |frame|
+      title = "Translation #{frame.to_s.rjust(2)}"
+      puts seq.translate(frame).to_fasta(title, 60)
+    end
+  end
+
+
+  # Displays some basic properties of the sequence.
+  def seqstat(str)
+    max = 150
+    seq = getseq(str)
+    rep = "\n* * * Sequence statistics * * *\n\n"
+    if seq.moltype == Bio::Sequence::NA
+      fwd = seq
+      rev = seq.complement
+      if seq.length > max
+        dot = " ..."
+        fwd = fwd.subseq(1, max)
+        rev = rev.subseq(1, max)
+      end
+      rep << "5'->3' sequence   : #{fwd.fold(70,20).strip}#{dot}\n"
+      rep << "3'->5' sequence   : #{rev.fold(70,20).strip}#{dot}\n"
+      [ 1, 2, 3, -1, -2, -3 ].each do |frame|
+        pep = seq.subseq(1, max+2).translate(frame).fold(70,20).strip
+        rep << "Translation  #{frame.to_s.rjust(2)}   : #{pep}#{dot}\n"
+      end
+      rep << "Length            : #{seq.length} bp\n"
+      rep << "GC percent        : #{seq.gc_percent} %\n"
+
+      ary = []
+      seq.composition.sort.each do |base, num|
+        percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
+        count   = num.to_s.rjust(seq.length.to_s.length)
+        ary << "                    #{base} - #{count} (#{percent} %)\n"
+      end
+      rep << "Composition       : #{ary.join.strip}\n"
+
+      rep << "Codon usage       :\n"
+      hash = Hash.new("0.0%")
+      seq.codon_usage.sort.each do |codon, num|
+        percent = format("%.1f%", 100.0 * num / (seq.length / 3))
+        hash[codon] = percent
+      end
+      rep << codontable(1, hash).output
+
+      begin
+        rep << "Molecular weight  : #{seq.molecular_weight}\n"
+      rescue
+        rep << "Molecular weight  : #{$!}\n"
+      end
+      begin
+        rep << "Protein weight    : #{seq.translate.chomp('*').molecular_weight}\n"
+      rescue
+        rep << "Protein weight    : #{$!}\n"
+      end
+    else
+      pep = seq
+      if seq.length > max
+        dot = " ..."
+        pep = seq.subseq(1, max)
+      end
+      rep << "N->C sequence     : #{pep.fold(70,20).strip}#{dot}\n"
+      rep << "Length            : #{seq.length} aa\n"
+
+      names = Bio::AminoAcid.names
+      ary = []
+      seq.composition.sort.each do |aa, num|
+        percent = format("%.2f", 100.0 * num / seq.length).rjust(6)
+        count   = num.to_s.rjust(seq.length.to_s.length)
+        code    = names[aa]
+        name    = names[names[aa]]
+        ary << "                    #{aa} #{code} - #{count} (#{percent} %) #{name}\n"
+      end
+      rep << "Composition       : #{ary.join.strip}\n"
+
+      begin
+        rep << "Protein weight    : #{seq.molecular_weight}\n"
+      rescue
+        rep << "Protein weight    : #{$!}\n"
+      end
+    end
+    rep  << "//\n"
+    puts rep
+    return rep
+  end
+
+  # Displays a DNA sequence by ascii art in B-type double helix.
+  # Argument need to be at least 16 bases in length.
+  def doublehelix(str)
+    seq = getseq(str)
+    if seq.length < 16
+      warn "Error: Sequence must be longer than 16 bases."
+      return
+    end
+    if seq.moltype != Bio::Sequence::NA
+      warn "Error: Sequence must be a DNA sequence."
+      return
+    end
+    pairs = [ [5, 0], [4, 2], [3, 3], [2, 4], 
+              [1, 4], [0, 3], [0, 2], [1, 0] ]
+    seq.window_search(16, 16) do |subseq|
+      pairs.each_with_index do |ij, x|
+        base = subseq[x, 1]
+        puts ' ' * ij[0] + base + '-' * ij[1] + base.complement + "\n"
+      end
+      pairs.reverse.each_with_index do |ij, x|
+        base = subseq[x + 8, 1]
+        puts ' ' * ij[0] + base.complement + '-' * ij[1] + base + "\n"
+      end
+    end
+  end
+
+end
+
+
+class String
+
+  def step(window_size)
+    i = 0
+    0.step(self.length - window_size, window_size) do |i|
+      yield self[i, window_size]
+    end
+    yield self[i + window_size .. -1] if i + window_size < self.length
+  end
+
+  def skip(window_size, step_size = 1)
+    i = 0
+    0.step(self.length - window_size, step_size) do |i|
+      yield [self[i, window_size], i + 1, i + window_size]
+    end
+    from = i + step_size
+    to  = [self.length, i + step_size + window_size].min
+    yield [self[from, window_size], from + 1, to] if from + 1 <= to
+  end
+
+  def to_naseq
+    Bio::Sequence::NA.new(self)
+  end
+
+  def to_aaseq
+    Bio::Sequence::AA.new(self)
+  end
+
+  # folding both line end justified
+  def fold(fill_column = 72, indent = 0)
+    str = ''
+
+    # size : allowed length of the actual text
+    unless (size = fill_column - indent) > 0
+      warn "Error: indent > fill_column (indent is set to 0)"
+      size = fill_column
+      indent = 0
+    end
+
+    0.step(self.length - 1, size) do |n|
+      str << ' ' * indent + self[n, size] + "\n"
+    end
+
+    return str
+  end
+
+  # folding with conscious about word boundaries with prefix string
+  def fill(fill_column = 80, indent = 0, separater = ' ', prefix = '', first_line_only = true)
+
+    # size : allowed length of the actual text
+    unless (size = fill_column - indent) > 0
+      warn "Error: indent > fill_column (indent is set to 0)"
+      size = fill_column
+      indent = 0
+    end
+
+    n = pos = 0
+    ary = []
+    while n < self.length
+      pos = self[n, size].rindex(separater)
+
+      if self[n, size].length < size    # last line of the folded str
+        pos = nil
+      end
+
+      if pos
+        ary << self[n, pos+separater.length]
+        n += pos + separater.length
+      else                              # line too long or the last line
+        ary << self[n, size]
+        n += size
+      end
+    end
+    str = ary.join("\n")
+
+    str[0,0] = prefix + ' ' * (indent - prefix.length)
+    if first_line_only
+      head = ' ' * indent
+    else
+      head = prefix + ' ' * (indent - prefix.length)
+    end
+    str.gsub!("\n", "\n#{head}")
+
+    return str.chomp
+  end
+end
+

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

@@ -0,0 +1,87 @@
+#
+# = bio/shell/plugin/soap.rb - web services
+#
+# Copyright::   Copyright (C) 2006
+#               Toshiaki Katayama <k@bioruby.org>
+# License::     Ruby's
+#
+# $Id: soap.rb,v 1.1 2007/07/09 11:17:09 k Exp $
+#
+
+module Bio::Shell
+
+  private
+
+  def ncbisoap(wsdl = nil)
+    if wsdl
+      @ncbisoap = Bio::NCBI::SOAP.new(wsdl)
+    else
+      @ncbisoap ||= Bio::NCBI::SOAP.new
+    end
+    return @ncbisoap
+  end
+
+  def ebisoap(wsdl = nil)
+    case wsdl
+    when :ipscan
+      @ebisoap = Bio::EBI::SOAP::InterProScan.new(wsdl)
+    when :emboss
+      @ebisoap = Bio::EBI::SOAP::Emboss.new(wsdl)
+    when :clustalw
+      @ebisoap = Bio::EBI::SOAP::ClustalW.new(wsdl)
+    when :tcoffee
+      @ebisoap = Bio::EBI::SOAP::TCoffee.new(wsdl)
+    when :muscle
+      @ebisoap = Bio::EBI::SOAP::Muscle.new(wsdl)
+    when :fasta
+      @ebisoap = Bio::EBI::SOAP::Fasta.new(wsdl)
+    when :wublast
+      @ebisoap = Bio::EBI::SOAP::WUBlast.new(wsdl)
+    when :mpsrch
+      @ebisoap = Bio::EBI::SOAP::MPsrch.new(wsdl)
+    when :scanps
+      @ebisoap = Bio::EBI::SOAP::ScanPS.new(wsdl)
+    when :msd
+      @ebisoap = Bio::EBI::SOAP::MSD.new(wsdl)
+    when :ontology
+      @ebisoap = Bio::EBI::SOAP::Ontology.new(wsdl)
+    when :citation
+      @ebisoap = Bio::EBI::SOAP::Citation.new(wsdl)
+    when /^http/
+      @ebisoap = Bio::EBI::SOAP.new(wsdl)
+    else
+      @ebisoap ||= Bio::EBI::SOAP.new
+    end
+    return @ebisoap
+  end
+
+  def ddbjsoap(wsdl = nil)
+    case wsdl
+    when :blast
+      @ddbjsoap = Bio::DDBJ::XML::Blast.new
+    when :fasta
+      @ddbjsoap = Bio::DDBJ::XML::Fasta.new
+    when :clustalw
+      @ddbjsoap = Bio::DDBJ::XML::ClustalW.new
+    when :ddbj
+      @ddbjsoap = Bio::DDBJ::XML::DDBJ.new
+    when :gib
+      @ddbjsoap = Bio::DDBJ::XML::Gib.new
+    when :gtop
+      @ddbjsoap = Bio::DDBJ::XML::Gtop.new
+    when :pml
+      @ddbjsoap = Bio::DDBJ::XML::PML.new
+    when :srs
+      @ddbjsoap = Bio::DDBJ::XML::SRS.new
+    when :txsearch
+      @ddbjsoap = Bio::DDBJ::XML::TxSearch.new
+    when /^http/
+      @ddbjsoap = Bio::DDBJ::XML.new(wsdl)
+    else
+      @ddbjsoap ||= Bio::DDBJ::XML.new
+    end
+    return @ddbjsoap
+  end
+
+end
+

data/lib/bio/shell/rails/vendor/plugins/bioruby/generators/bioruby/bioruby_generator.rb

@@ -0,0 +1,29 @@
+class BiorubyGenerator < Rails::Generator::Base
+  def manifest
+    record do |m|
+      m.directory 'app/controllers'
+      m.directory 'app/helpers'
+      m.directory 'app/views/bioruby'
+      m.directory 'app/views/layouts'
+      m.directory 'public/images/bioruby'
+      m.directory 'public/stylesheets'
+      m.file 'bioruby_controller.rb', 'app/controllers/bioruby_controller.rb'
+      m.file 'bioruby_helper.rb',     'app/helpers/bioruby_helper.rb'
+      m.file '_methods.rhtml',        'app/views/bioruby/_methods.rhtml'
+      m.file '_classes.rhtml',        'app/views/bioruby/_classes.rhtml'
+      m.file '_modules.rhtml',        'app/views/bioruby/_modules.rhtml'
+      m.file '_log.rhtml',            'app/views/bioruby/_log.rhtml'
+      m.file '_variables.rhtml',      'app/views/bioruby/_variables.rhtml'
+      m.file 'commands.rhtml',        'app/views/bioruby/commands.rhtml'
+      m.file 'history.rhtml',         'app/views/bioruby/history.rhtml'
+      m.file 'index.rhtml',           'app/views/bioruby/index.rhtml'
+      m.file 'bioruby.rhtml',         'app/views/layouts/bioruby.rhtml'
+      m.file 'spinner.gif',           'public/images/bioruby/spinner.gif'
+      m.file 'bioruby-gem.png',       'public/images/bioruby/gem.png'
+      m.file 'bioruby-link.gif',      'public/images/bioruby/link.gif'
+      m.file 'bioruby-bg.gif',        'public/images/bioruby/bg.gif'
+      m.file 'bioruby.css',           'public/stylesheets/bioruby.css'
+    end
+  end
+end
+