Class | Bio::Shell::Demo
In: | lib/bio/shell/demo.rb
Parent: | Object

### Methods

aldh2 all entry mito new pdb pdb_hetdic sequence shell tutorial

### Public Class methods

new()

[Source]

        # File lib/bio/shell/demo.rb, line 26
    26:     def initialize
    27:       @bind = Bio::Shell.cache[:binding]
    28:     end

### Public Instance methods

aldh2()

[Source]

        # File lib/bio/shell/demo.rb, line 41
    41:     def aldh2
    42:     end

all()

[Source]

        # File lib/bio/shell/demo.rb, line 30
    30:     def all
    31:       sequence &&
    32:       entry &&
    33:       shell &&
    34:       pdb &&
    35:       true
    36:     end

entry()

[Source]

        # 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

mito()

[Source]

        # 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

pdb()

[Source]

         # 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

pdb_hetdic()

[Source]

         # 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

sequence()

[Source]

        # 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

shell()

[Source]

        # File lib/bio/shell/demo.rb, line 84
    84:     def shell
    85:       run(%q[pwd], "Show current working directory ...", false) &&
    86:       run(%q[dir], "Show directory contents ...", false) &&
    87:       run(%q[dir "shell/session"], "Show directory contents ...", false) &&
    88:       true
    89:     end

tutorial()

[Source]

        # File lib/bio/shell/demo.rb, line 38
    38:     def tutorial
    39:     end

[Validate]