Class: Bio::Shell::Demo

Inherits:
Object show all
Defined in:
lib/bio/shell/demo.rb

Instance Method Summary collapse

Constructor Details

#initializeDemo



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# File 'lib/bio/shell/demo.rb', line 26

def initialize
  @bind = Bio::Shell.cache[:binding]
end

Instance Method Details

#aldh2Object



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# File 'lib/bio/shell/demo.rb', line 41

def aldh2
end

#allObject



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# File 'lib/bio/shell/demo.rb', line 30

def all
  sequence &&
  entry &&
  shell &&
  pdb &&
  true
end

#entryObject



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# File 'lib/bio/shell/demo.rb', line 75

def entry
  run(%q[kuma = getobj("gb:AF237819")], "Obtain an entry from GenBank database", false) &&
  run(%q[kuma.definition], "Definition of the entry", true) &&
  run(%q[kuma.naseq], "Sequence of the entry", true) &&
  run(%q[kuma.naseq.translate], "Translate the sequence to protein", true) &&
  run(%q[midifile("data/AF237819.mid", kuma.naseq)], "Generate gene music ...", false) &&
  true
end

#mitoObject



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# File 'lib/bio/shell/demo.rb', line 44

def mito
  run(%q[entry = getent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) &&
  run(%q[disp entry], "Check the contents ...", false) &&
  run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) &&
  run(%q[web], "Start BioRuby on Rails...", false) &&
  run(%q[puts kuma.entry_id], "Extract entry ID ...", false) &&
  run(%q[puts kuma.definition], "Extract definition ...", false) &&
  run(%q[gene = kuma.seq], "Extract DNA sequence of the gene ...", true) &&
  run(%q[doublehelix(gene)], "Show the sequence in ascii art ...", false) &&
  run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
  run(%q[config :color], "Change to color mode...", false) &&
  run(%q[seqstat(gene)], "Statistics of the gene ...", false) &&
  #run(%q[codontable], "Codontalble ...", false) &&
  run(%q[protein = gene.translate], "Translate DNA into protein ...", true) &&
  run(%q[comp = protein.composition], "Composition of the amino acids ...", false) &&
  run(%q[pp comp], "Check the composition ...", false) &&
  run(%q[puts protein.molecular_weight], "Molecular weight ...", false) &&
  run(%q[midifile("data/kumamushi.mid", gene)], "Gene to music ...", false) &&
  run(%q[`open "data/kumamushi.mid"`], "Let's listen ...", false) &&
  true
end

#pdbObject



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# File 'lib/bio/shell/demo.rb', line 91

def pdb
  run(%q[ent_1bl8 = getent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) &&
  run(%q[head ent_1bl8], "Head part of the entry ...", false) &&
  run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) &&
  run(%q[disp "data/1bl8.pdb"], "Look through the entire entry ...", false) &&
  run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) &&
  run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) &&
  run(%q[pdb_1bl8.each_heterogen { |heterogen| p heterogen.resName }], "Showing each heterogen object ...", false) &&
  true
end

#pdb_hetdicObject



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# File 'lib/bio/shell/demo.rb', line 102

def pdb_hetdic
#      run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read],
#          "Retrieving the het_dic database ...", false) &&
#      run(%q[savefile("data/het_dictionary.txt", het_dic)],
#          "Saving the file ... ", false) &&
  run(%q[het_dic.size], "Bytes of the file ...", true) &&
  run(%q[disp "data/het_dictionary.txt"], "Take a look on the contents ...", true) &&
  run(%q[flatindex("het_dic", "data/het_dictionary.txt")],
      "Creating index to make the seaarchable database ...", false) &&
  run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) &&
  run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) &&
  run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) &&
  true
end

#sequenceObject



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# File 'lib/bio/shell/demo.rb', line 66

def sequence
  run(%q[dna = getseq("atgc" * 100)], "Generating DNA sequence ...", true) &&
  run(%q[doublehelix dna], "Double helix representation", false) &&
  run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) &&
  run(%q[protein.molecular_weight], "Calculating molecular weight ...", true) &&
  run(%q[protein.composition], "Amino acid composition ...", true) &&
  true
end

#shellObject



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# File 'lib/bio/shell/demo.rb', line 84

def shell
  run(%q[pwd], "Show current working directory ...", false) &&
  run(%q[dir], "Show directory contents ...", false) &&
  run(%q[dir "shell/session"], "Show directory contents ...", false) &&
  true
end

#tutorialObject



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# File 'lib/bio/shell/demo.rb', line 38

def tutorial
end