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

Classes and Modules

Class Bio::Blast::Default::Report::HSP
Class Bio::Blast::Default::Report::Hit
Class Bio::Blast::Default::Report::Iteration

Constants

DELIMITER	=	RS = "\nBLAST"		Delimiter of each entry. Bio::FlatFile uses it.
DELIMITER_OVERRUN	=	5		(Integer) excess read size included in DELIMITER.

Attributes

db_len	[R]	number of letters in database
db_num	[R]	number of sequences in database
eff_space	[R]	effective length of the database
entry_overrun	[R]	piece of next entry. Bio::FlatFile uses it.
expect	[R]	e-value threshold specified when BLAST was executed
gap_extend	[R]	gap extend penalty
gap_open	[R]	gap open penalty
iterations	[R]	(PSI-BLAST) Returns iterations. It returns an array of Bio::Blast::Default::Report::Iteration class. Note that normal blastall result usually contains one iteration.
matrix	[R]	name of the matrix
num_hits	[R]	number of hits. Note that this may differ from `hits.size`.
posted_date	[R]	posted date of the database
sc_match	[R]	match score of the matrix
sc_mismatch	[R]	mismatch score of the matrix

Public Class methods

new(str)

Creates a new Report object from BLAST result text.

[Source]

    # File lib/bio/appl/blast/format0.rb, line 53
53:         def initialize(str)
54:           str = str.sub(/\A\s+/, '')
55:           str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
56:           @entry_overrun = $1
57:           @entry = str
58:           data = str.split(/(?:^[ \t]*\n)+/)
59: 
60:           format0_split_headers(data)
61:           @iterations = format0_split_search(data)
62:           format0_split_stat_params(data)
63:         end

open(filename, *mode)

Opens file by using Bio::FlatFile.open.

[Source]

    # File lib/bio/appl/blast/format0.rb, line 48
48:         def self.open(filename, *mode)
49:           Bio::FlatFile.open(self, filename, *mode)
50:         end

Public Instance methods

converged?()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 221
221:         def converged?
222:           @iterations.last.converged?
223:         end

db()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 245
245:         def db
246:           unless defined?(@db)
247:             if /Database *\: *(.*)/m =~ @f0database then
248:               a = $1.split(/^/)
249:               a.pop if a.size > 1
250:               @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
251:             end
252:           end #unless
253:           @db
254:         end

each()

Alias for each_hit

each_hit() {|x| ...}

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.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 196
196:         def each_hit
197:           @iterations.last.each do |x|
198:             yield x
199:           end
200:         end

each_iteration() {|x| ...}

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 186
186:         def each_iteration
187:           @iterations.each do |x|
188:             yield x
189:           end
190:         end

entropy()

Same as iterations.last.entropy.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 146
146:         def entropy;        @iterations.last.entropy;        end

gapped_entropy()

Same as iterations.last.gapped_entropy.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 153
153:         def gapped_entropy; @iterations.last.gapped_entropy; end

gapped_kappa()

Same as iterations.last.gapped_kappa.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 149
149:         def gapped_kappa;   @iterations.last.gapped_kappa;   end

gapped_lambda()

Same as iterations.last.gapped_lambda.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 151
151:         def gapped_lambda;  @iterations.last.gapped_lambda;  end

hits()

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.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 207
207:         def hits
208:           @iterations.last.hits
209:         end

kappa()

Same as iterations.last.kappa.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 142
142:         def kappa;          @iterations.last.kappa;          end

lambda()

Same as iterations.last.lambda.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 144
144:         def lambda;         @iterations.last.lambda;         end

message()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 213
213:         def message
214:           @iterations.last.message
215:         end

pattern()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 173
173:         def pattern; @iterations.first.pattern; end

pattern_positions()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 178
178:         def pattern_positions
179:           @iterations.first.pattern_positions
180:         end

program()

Returns program name.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 156
156:         def program;        format0_parse_header; @program;        end

query_def()

Returns definition of the query.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 168
168:         def query_def; format0_parse_query; @query_def; end

query_len()

Returns length of the query.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 165
165:         def query_len; format0_parse_query; @query_len; end

reference()

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.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 229
229:         def reference
230:           references[0]
231:         end

references()

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

[Source]

     # File lib/bio/appl/blast/format0.rb, line 235
235:         def references
236:           unless defined?(@references)
237:             @references = @f0references.collect do |x|
238:               x.to_s.gsub(/\s+/, ' ').strip
239:             end
240:           end #unless
241:           @references
242:         end

to_s()

Returns whole entry as a string.

[Source]

    # File lib/bio/appl/blast/format0.rb, line 74
74:         def to_s; @entry; end

version()

Returns version of the program.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 158
158:         def version;        format0_parse_header; @version;        end

version_date()

Returns released date of the program.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 162
162:         def version_date;   format0_parse_header; @version_date;   end

version_number()

Returns version number string of the program.

[Source]

     # File lib/bio/appl/blast/format0.rb, line 160
160:         def version_number; format0_parse_header; @version_number; end

Methods

Classes and Modules

Constants

Attributes

Public Class methods

Public Instance methods