Class: Genfrag::App::IndexCommand

Inherits:
Command
  • Object
show all
Defined in:
lib/genfrag/app/index_command.rb,
lib/genfrag/app/index_command/db.rb

Defined Under Namespace

Classes: DB

Instance Attribute Summary collapse

Attributes inherited from Command

#ops, #options

Instance Method Summary collapse

Methods inherited from Command

#cli_p, #clierr_p, #initialize, #standard_options

Constructor Details

This class inherits a constructor from Genfrag::App::Command

Instance Attribute Details

#sizes ⇒ Object (readonly)

Returns the value of attribute sizes.



7
8
9
 
# File 'lib/genfrag/app/index_command.rb', line 7

def sizes
  @sizes
end

Instance Method Details

#cli_run(args) ⇒ Object

Run from command-line



11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
 
# File 'lib/genfrag/app/index_command.rb', line 11

def cli_run( args )
  parse args

  @input_filenames = ARGV

  validate_options(options)

  if options[:tracktime]
    Genfrag.tracktime {
      run(options, @input_filenames, true)
    }
  else
    run(options, @input_filenames, true)
  end

end

#opt_parser ⇒ Object

Option parser for command-line



147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
 
# File 'lib/genfrag/app/index_command.rb', line 147

def opt_parser
  std_opts = standard_options

  opts = OptionParser.new
  opts.banner = 'Usage: genfrag index [options]'

  opts.separator ''
  opts.separator "  Create a database of sequence fragments that match the last 5' fragment"
  opts.separator "  cut by two restricting enzymes RE3 and RE5."
  opts.separator "  The Fasta file defined by the --fasta option is taken as input."
  opts.separator "  Two files are created for the search function - a lookup file, and"
  opts.separator "  the contents of the Fasta file rewritten in a special format. You can"
  opts.separator "  specify the name of the lookup file with the --lookup option."

  opts.separator ''

  ary = [:verbose, :quiet, :tracktime, :indir, :outdir, :sqlite, :re5, :re3,
    :filelookup, :filefasta
  ]
  ary.each { |a| opts.on(*std_opts[a]) }

  opts.separator ''
  opts.separator '  Common Options:'
  opts.on( '-h', '--help', 'show this message' ) { @out.puts opts; exit 1 }
  opts.separator '  Examples:'
  opts.separator '    genfrag index -f example.fasta --re5 BstYI --re3 MseI'
  opts.separator '    genfrag index --out /tmp --in . -f example.fasta --re5 BstYI --re3 MseI'
  opts
end

#parse(args) ⇒ Object

Parse options passed from command-line



179
180
181
182
183
184
185
186
187
188
189
 
# File 'lib/genfrag/app/index_command.rb', line 179

def parse( args )
  opts = opt_parser

  if args.empty?
    @out.puts opts
    exit 1
  end

# parse the command line arguments
  opts.parse! args
end

#run(ops = @ops, input_filenames = [], cli = false) ⇒ Object

Main class for creating the index - accepts multiple input files. Either an SQLite database or a flat file index is created (extension .tdf) which is unique for the input file combination. This file is used by the Search routine later.



32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
 
# File 'lib/genfrag/app/index_command.rb', line 32

def run(ops=@ops, input_filenames=[], cli=false)
  if ops.kind_of? OpenStruct
    @ops = ops.dup
  elsif ops.kind_of? Hash
    @ops = OpenStruct.new(ops)
  else
    raise ArgumentError
  end
  
# Set defaults
  @ops.verbose    ||= false
  @ops.quiet      ||= false
  @ops.sqlite     ||= false
  @ops.filelookup ||= nil
  @ops.filefasta  ||= nil
  @ops.re5        ||= nil
  @ops.re3        ||= nil
  @ops.indir      ||= '.'
  @ops.outdir     ||= '.'

  @input_filenames = input_filenames.empty? ? [@ops.filefasta] : input_filenames
  @sizes = {}    
  db = IndexCommand::DB.new(@ops, @input_filenames)
  @re5_ds, @re3_ds = [@ops.re5, @ops.re3].map {|x| Bio::RestrictionEnzyme::DoubleStranded.new(x)}
  db.write_headers    

  if @ops.verbose
    cli_p(cli, <<-END
RE5: #{@ops.re5}
#{@re5_ds.aligned_strands_with_cuts.primary}
#{@re5_ds.aligned_strands_with_cuts.complement}

RE3: #{@ops.re3}
#{@re3_ds.aligned_strands_with_cuts.primary}
#{@re3_ds.aligned_strands_with_cuts.complement}
END
)
  end

# unit test with aasi, aari, and ppii
  re5_regexp, re3_regexp = [@ops.re5, @ops.re3].map {|x| Bio::Sequence::NA.new( Bio::RestrictionEnzyme::DoubleStranded.new(x).aligned_strands.primary ).to_re }

  entries = {}
# Account for exact duplicate sequences
  @input_filenames.each do |input_filename|
    Bio::FlatFile.auto(File.join(@ops.indir, input_filename)).each_entry do |e|
      e.definition.tr!("\t",'')
      s = e.seq.to_s.downcase
      if entries[s]
        entries[s] << e.definition
      else
        entries[s] = [e.definition]
      end
    end
  end
  
  a_re = /(.*)(#{re5_regexp})/
  b_re = /(.*?)(#{re3_regexp})/
  
  normalized_fasta_id=0
  entries.each do |seq, definitions|
    normalized_fasta_id+=1
    db.write_entry_to_fasta(normalized_fasta_id, seq, definitions)
    
  # NOTE the index command is slow because of the match functions, compare with ruby 1.9
    m1 = a_re.match(seq)
    if m1
    # Find the fragment 'frag1' cut most right in seq with re5_regexp
      frag1 = $2 + m1.post_match          

      position = $1.size

      m2 = b_re.match( frag1 )

    # Now cut frag1 with re3_regexp resulting in frag2
      if m2
        @frag2 = $1 + $2
        if @ops.verbose
          cli_p(cli, <<-END
---
#{definitions.join("\n")}
#{@frag2}
END
)
        end
        @sizes[@frag2.size] ||= []
        @sizes[@frag2.size] << [position, normalized_fasta_id]
      end
    end

  end

  i=0
  @sizes.each do |size,info|
    i+=1
    db.write_entry_to_freq(i, size, info.map {|x| x.join(' ')}.join(', ') )
  end
  
  if @ops.verbose
    @sizes.each { |entry| cli_p(cli, entry.inspect) }
  else
    cli_p(cli, "Cut sites found: #{@sizes.values.flatten.size / 2}")
  end
  
  db.close
end

#validate_options(o) ⇒ Object

Validate options passed from the command-line



192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
 
# File 'lib/genfrag/app/index_command.rb', line 192

def validate_options(o)
  if o[:filefasta] == nil
    clierr_p "missing option: must supply fasta filename"
    exit 1
  end

  if o[:re5] == nil
    clierr_p "missing option: re5"
    exit 1
  end

  if o[:re3] == nil
    clierr_p "missing option: re3"
    exit 1
  end

  begin
    Bio::RestrictionEnzyme::DoubleStranded.new(o[:re3])
  rescue
    clierr_p "re3 is not an enzyme name"
    exit 1
  end

  begin
    Bio::RestrictionEnzyme::DoubleStranded.new(o[:re5])
  rescue
    clierr_p "re5 is not an enzyme name"
    exit 1
  end
end