Class | Bio::Blast::Default::Report
In: | lib/bio/appl/blast/format0.rb
Parent: | Object

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.

### Methods

converged? db each each_hit each_iteration entropy gapped_entropy gapped_kappa gapped_lambda hits kappa lambda message new open pattern pattern_positions program query_def query_len reference references to_s version version_date version_number

### 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 48
    48:         def initialize(str)
    49:           str = str.sub(/\A\s+/, '')
    50:           str.sub!(/\n(T?BLAST.*)/m, "\n") # remove trailing entries for sure
    51:           @entry_overrun = $1
    52:           @entry = str
    53:           data = str.split(/(?:^[ \t]*\n)+/)
    54:
    55:           format0_split_headers(data)
    56:           @iterations = format0_split_search(data)
    57:           format0_split_stat_params(data)
    58:         end

open(filename, *mode)

Opens file by using Bio::FlatFile.open.

[Source]

        # File lib/bio/appl/blast/format0.rb, line 43
    43:         def self.open(filename, *mode)
    44:           Bio::FlatFile.open(self, filename, *mode)
    45:         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 203
    203:         def converged?
    204:           @iterations.last.converged?
    205:         end

db()

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

[Source]

         # File lib/bio/appl/blast/format0.rb, line 227
    227:         def db
    228:           unless defined?(@db)
    229:             if /Database *\: *(.*)/m =~ @f0database then
    230:               a = $1.split(/^/)
    231:               a.pop if a.size > 1
    232:               @db = a.collect { |x| x.sub(/\s+\z/, '') }.join(' ')
    233:             end
    234:           end #unless
    235:           @db
    236:         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 178
    178:         def each_hit
    179:           @iterations.last.each do |x|
    180:             yield x
    181:           end
    182:         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 168
    168:         def each_iteration
    169:           @iterations.each do |x|
    170:             yield x
    171:           end
    172:         end

entropy()

Same as `iterations.last.entropy`.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 128
    128:         def entropy;        @iterations.last.entropy;        end

gapped_entropy()

Same as `iterations.last.gapped_entropy`.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 135
    135:         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 131
    131:         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 133
    133:         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 189
    189:         def hits
    190:           @iterations.last.hits
    191:         end

kappa()

Same as `iterations.last.kappa`.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 124
    124:         def kappa;          @iterations.last.kappa;          end

lambda()

Same as `iterations.last.lambda`.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 126
    126:         def lambda;         @iterations.last.lambda;         end

message()

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

[Source]

         # File lib/bio/appl/blast/format0.rb, line 195
    195:         def message
    196:           @iterations.last.message
    197:         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 155
    155:         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 160
    160:         def pattern_positions
    161:           @iterations.first.pattern_positions
    162:         end

program()

Returns program name.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 138
    138:         def program;        format0_parse_header; @program;        end

query_def()

Returns definition of the query.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 150
    150:         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 147
    147:         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 211
    211:         def reference
    212:           references[0]
    213:         end

references()

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

[Source]

         # File lib/bio/appl/blast/format0.rb, line 217
    217:         def references
    218:           unless defined?(@references)
    219:             @references = @f0references.collect do |x|
    220:               x.to_s.gsub(/\s+/, ' ').strip
    221:             end
    222:           end #unless
    223:           @references
    224:         end

to_s()

Returns whole entry as a string.

[Source]

        # File lib/bio/appl/blast/format0.rb, line 69
    69:         def to_s; @entry; end

version()

Returns version of the program.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 140
    140:         def version;        format0_parse_header; @version;        end

version_date()

Returns released date of the program.

[Source]

         # File lib/bio/appl/blast/format0.rb, line 144
    144:         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 142
    142:         def version_number; format0_parse_header; @version_number; end

[Validate]