Class: Bio::Blast::Default::Report

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/appl/blast/format0.rb

Overview

Bio::Blast::Default::Report parses NCBI BLAST default output and stores information in the data. It may store some Bio::Blast::Default::Report::Iteration objects.

Defined Under Namespace

Classes: AlwaysNil, F0dbstat, HSP, Hit, Iteration

Constant Summary collapse

DELIMITER =

Delimiter of each entry. Bio::FlatFile uses it.

RS = "\nBLAST"
DELIMITER_OVERRUN =

(Integer) excess read size included in DELIMITER.

5

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(*arg) ⇒ Report

def



53
54
55
56
57
58
59
60
61
62
63
 
# File 'lib/bio/appl/blast/format0.rb', line 53

def initialize(str)
  str = str.sub(/\A\s+/, '')
  str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
  @entry_overrun = $1
  @entry = str
  data = str.split(/(?:^[ \t]*\n)+/)

  format0_split_headers(data)
  @iterations = format0_split_search(data)
  format0_split_stat_params(data)
end

Instance Attribute Details

#db_len ⇒ Object (readonly)

number of letters in database



102
103
104
 
# File 'lib/bio/appl/blast/format0.rb', line 102

def db_len
  @db_len
end

#db_num ⇒ Object (readonly)

number of sequences in database



98
99
100
 
# File 'lib/bio/appl/blast/format0.rb', line 98

def db_num
  @db_num
end

#eff_space ⇒ Object (readonly)

effective length of the database



110
111
112
 
# File 'lib/bio/appl/blast/format0.rb', line 110

def eff_space
  @eff_space
end

#entry_overrun ⇒ Object (readonly)

piece of next entry. Bio::FlatFile uses it.



65
66
67
 
# File 'lib/bio/appl/blast/format0.rb', line 65

def entry_overrun
  @entry_overrun
end

#expect ⇒ Object (readonly)

e-value threshold specified when BLAST was executed



134
135
136
 
# File 'lib/bio/appl/blast/format0.rb', line 134

def expect
  @expect
end

#gap_extend ⇒ Object (readonly)

gap extend penalty



130
131
132
 
# File 'lib/bio/appl/blast/format0.rb', line 130

def gap_extend
  @gap_extend
end

#gap_open ⇒ Object (readonly)

gap open penalty



126
127
128
 
# File 'lib/bio/appl/blast/format0.rb', line 126

def gap_open
  @gap_open
end

#iterations ⇒ Object (readonly)

(PSI-BLAST) Returns iterations. It returns an array of Bio::Blast::Default::Report::Iteration class. Note that normal blastall result usually contains one iteration.



71
72
73
 
# File 'lib/bio/appl/blast/format0.rb', line 71

def iterations
  @iterations
end

#matrix ⇒ Object (readonly)

name of the matrix



114
115
116
 
# File 'lib/bio/appl/blast/format0.rb', line 114

def matrix
  @matrix
end

#num_hits ⇒ Object (readonly)

number of hits. Note that this may differ from hits.size.



138
139
140
 
# File 'lib/bio/appl/blast/format0.rb', line 138

def num_hits
  @num_hits
end

#posted_date ⇒ Object (readonly)

posted date of the database



106
107
108
 
# File 'lib/bio/appl/blast/format0.rb', line 106

def posted_date
  @posted_date
end

#sc_match ⇒ Object (readonly)

match score of the matrix



118
119
120
 
# File 'lib/bio/appl/blast/format0.rb', line 118

def sc_match
  @sc_match
end

#sc_mismatch ⇒ Object (readonly)

mismatch score of the matrix



122
123
124
 
# File 'lib/bio/appl/blast/format0.rb', line 122

def sc_mismatch
  @sc_mismatch
end

Class Method Details

.open(filename, *mode) ⇒ Object

Opens file by using Bio::FlatFile.open.



48
49
50
 
# File 'lib/bio/appl/blast/format0.rb', line 48

def self.open(filename, *mode)
  Bio::FlatFile.open(self, filename, *mode)
end

Instance Method Details

#converged? ⇒ Boolean

(PSI-BLAST) Same as iterations.last.converged?. Returns true if the last iteration is converged, otherwise, returns false.

Returns:

  • (Boolean) 


221
222
223
 
# File 'lib/bio/appl/blast/format0.rb', line 221

def converged?
  @iterations.last.converged?
end

#db ⇒ Object

Returns the name (filename or title) of the database.



245
246
247
248
249
250
251
252
253
254
 
# File 'lib/bio/appl/blast/format0.rb', line 245

def db
  unless defined?(@db)
    if /Database *\: *(.*)/m =~ @f0database then
      a = $1.split(/^/)
      a.pop if a.size > 1
      @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
    end
  end #unless
  @db
end

#each_hit ⇒ Object Also known as: each

Iterates over each hit of the last iteration. Same as iterations.last.each_hit. Yields a Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.



196
197
198
199
200
 
# File 'lib/bio/appl/blast/format0.rb', line 196

def each_hit
  @iterations.last.each do |x|
    yield x
  end
end

#each_iteration ⇒ Object

(PSI-BLAST) Iterates over each iteration. Same as iterations.each. Yields a Bio::Blast::Default::Report::Iteration object.



186
187
188
189
190
 
# File 'lib/bio/appl/blast/format0.rb', line 186

def each_iteration
  @iterations.each do |x|
    yield x
  end
end

#entropy ⇒ Object

Same as iterations.last.entropy.



146
 
# File 'lib/bio/appl/blast/format0.rb', line 146

def entropy;        @iterations.last.entropy;        end

#gapped_entropy ⇒ Object

Same as iterations.last.gapped_entropy.



153
 
# File 'lib/bio/appl/blast/format0.rb', line 153

def gapped_entropy; @iterations.last.gapped_entropy; end

#gapped_kappa ⇒ Object

Same as iterations.last.gapped_kappa.



149
 
# File 'lib/bio/appl/blast/format0.rb', line 149

def gapped_kappa;   @iterations.last.gapped_kappa;   end

#gapped_lambda ⇒ Object

Same as iterations.last.gapped_lambda.



151
 
# File 'lib/bio/appl/blast/format0.rb', line 151

def gapped_lambda;  @iterations.last.gapped_lambda;  end

#hits ⇒ Object

Same as iterations.last.hits. Returns the last iteration’s hits. Returns an array of Bio::Blast::Default::Report::Hit object. This is very useful in most cases, e.g. for blastall results.



207
208
209
 
# File 'lib/bio/appl/blast/format0.rb', line 207

def hits
  @iterations.last.hits
end

#kappa ⇒ Object

Same as iterations.last.kappa.



142
 
# File 'lib/bio/appl/blast/format0.rb', line 142

def kappa;          @iterations.last.kappa;          end

#lambda ⇒ Object

Same as iterations.last.lambda.



144
 
# File 'lib/bio/appl/blast/format0.rb', line 144

def lambda;         @iterations.last.lambda;         end

#message ⇒ Object

(PSI-BLAST) Same as iterations.last.message.



213
214
215
 
# File 'lib/bio/appl/blast/format0.rb', line 213

def message
  @iterations.last.message
end

#pattern ⇒ Object

(PHI-BLAST) Same as iterations.first.pattern. Note that it returns the FIRST iteration’s value.



173
 
# File 'lib/bio/appl/blast/format0.rb', line 173

def pattern; @iterations.first.pattern; end

#pattern_positions ⇒ Object

(PHI-BLAST) Same as iterations.first.pattern_positions. Note that it returns the FIRST iteration’s value.



178
179
180
 
# File 'lib/bio/appl/blast/format0.rb', line 178

def pattern_positions
  @iterations.first.pattern_positions
end

#program ⇒ Object

Returns program name.



156
 
# File 'lib/bio/appl/blast/format0.rb', line 156

def program;        format0_parse_header; @program;        end

#query_def ⇒ Object

Returns definition of the query.



168
 
# File 'lib/bio/appl/blast/format0.rb', line 168

def query_def; format0_parse_query; @query_def; end

#query_len ⇒ Object

Returns length of the query.



165
 
# File 'lib/bio/appl/blast/format0.rb', line 165

def query_len; format0_parse_query; @query_len; end

#reference ⇒ Object

Returns the bibliography reference of the BLAST software. Note that this method shows only the first reference. When you want to get additional references, you can use references method.



229
230
231
 
# File 'lib/bio/appl/blast/format0.rb', line 229

def reference
  references[0]
end

#references ⇒ Object

Returns the bibliography references of the BLAST software. Returns an array of strings.



235
236
237
238
239
240
241
242
 
# File 'lib/bio/appl/blast/format0.rb', line 235

def references
  unless defined?(@references)
    @references = @f0references.collect do |x|
      x.to_s.gsub(/\s+/, ' ').strip
    end
  end #unless
  @references
end

#to_s ⇒ Object

Returns whole entry as a string.



74
 
# File 'lib/bio/appl/blast/format0.rb', line 74

def to_s; @entry; end

#version ⇒ Object

Returns version of the program.



158
 
# File 'lib/bio/appl/blast/format0.rb', line 158

def version;        format0_parse_header; @version;        end

#version_date ⇒ Object

Returns released date of the program.



162
 
# File 'lib/bio/appl/blast/format0.rb', line 162

def version_date;   format0_parse_header; @version_date;   end

#version_number ⇒ Object

Returns version number string of the program.



160
 
# File 'lib/bio/appl/blast/format0.rb', line 160

def version_number; format0_parse_header; @version_number; end