Class | Bio::Shell::Demo |
In: |
lib/bio/shell/demo.rb
|
Parent: | Object |
# File lib/bio/shell/demo.rb, line 26 26: def initialize 27: @bind = Bio::Shell.cache[:binding] 28: end
# File lib/bio/shell/demo.rb, line 30 30: def all 31: sequence && 32: entry && 33: shell && 34: pdb && 35: true 36: end
# File lib/bio/shell/demo.rb, line 75 75: def entry 76: run(%q[kuma = getobj("gb:AF237819")], "Obtain an entry from GenBank database", false) && 77: run(%q[kuma.definition], "Definition of the entry", true) && 78: run(%q[kuma.naseq], "Sequence of the entry", true) && 79: run(%q[kuma.naseq.translate], "Translate the sequence to protein", true) && 80: run(%q[midifile("data/AF237819.mid", kuma.naseq)], "Generate gene music ...", false) && 81: true 82: end
# File lib/bio/shell/demo.rb, line 44 44: def mito 45: run(%q[entry = getent("data/kumamushi.gb")], "Load kumamushi gene from GenBank database entry ...", false) && 46: run(%q[disp entry], "Check the contents ...", false) && 47: run(%q[kuma = flatparse(entry)], "Parse the database entry ...", true) && 48: run(%q[web], "Start BioRuby on Rails...", false) && 49: run(%q[puts kuma.entry_id], "Extract entry ID ...", false) && 50: run(%q[puts kuma.definition], "Extract definition ...", false) && 51: run(%q[gene = kuma.seq], "Extract DNA sequence of the gene ...", true) && 52: run(%q[doublehelix(gene)], "Show the sequence in ascii art ...", false) && 53: run(%q[seqstat(gene)], "Statistics of the gene ...", false) && 54: run(%q[config :color], "Change to color mode...", false) && 55: run(%q[seqstat(gene)], "Statistics of the gene ...", false) && 56: #run(%q[codontable], "Codontalble ...", false) && 57: run(%q[protein = gene.translate], "Translate DNA into protein ...", true) && 58: run(%q[comp = protein.composition], "Composition of the amino acids ...", false) && 59: run(%q[pp comp], "Check the composition ...", false) && 60: run(%q[puts protein.molecular_weight], "Molecular weight ...", false) && 61: run(%q[midifile("data/kumamushi.mid", gene)], "Gene to music ...", false) && 62: run(%q[`open "data/kumamushi.mid"`], "Let's listen ...", false) && 63: true 64: end
# File lib/bio/shell/demo.rb, line 91 91: def pdb 92: run(%q[ent_1bl8 = getent("pdb:1bl8")], "Retrieving PDB entry 1BL8 ...", false) && 93: run(%q[head ent_1bl8], "Head part of the entry ...", false) && 94: run(%q[savefile("1bl8.pdb", ent_1bl8)], "Saving the original entry in file ...", false) && 95: run(%q[disp "data/1bl8.pdb"], "Look through the entire entry ...", false) && 96: run(%q[pdb_1bl8 = flatparse(ent_1bl8)], "Parsing the entry ...", false) && 97: run(%q[pdb_1bl8.entry_id], "Showing the entry ID ...", true) && 98: run(%q[pdb_1bl8.each_heterogen { |heterogen| p heterogen.resName }], "Showing each heterogen object ...", false) && 99: true 100: end
# File lib/bio/shell/demo.rb, line 102 102: def pdb_hetdic 103: # run(%q[het_dic = open("http://deposit.pdb.org/het_dictionary.txt").read], 104: # "Retrieving the het_dic database ...", false) && 105: # run(%q[savefile("data/het_dictionary.txt", het_dic)], 106: # "Saving the file ... ", false) && 107: run(%q[het_dic.size], "Bytes of the file ...", true) && 108: run(%q[disp "data/het_dictionary.txt"], "Take a look on the contents ...", true) && 109: run(%q[flatindex("het_dic", "data/het_dictionary.txt")], 110: "Creating index to make the seaarchable database ...", false) && 111: run(%q[ethanol = flatsearch("het_dic", "EOH")], "Search an ethanol entry ...", true) && 112: run(%q[osake = flatparse(ethanol)], "Parse the entry ...", true) && 113: run(%q[osake.conect], "Showing connect table (conect) of the molecule ...", true) && 114: true 115: end
# File lib/bio/shell/demo.rb, line 66 66: def sequence 67: run(%q[dna = getseq("atgc" * 100)], "Generating DNA sequence ...", true) && 68: run(%q[doublehelix dna], "Double helix representation", false) && 69: run(%q[protein = dna.translate], "Translate DNA into Protein ...", true) && 70: run(%q[protein.molecular_weight], "Calculating molecular weight ...", true) && 71: run(%q[protein.composition], "Amino acid composition ...", true) && 72: true 73: end