### Home Classes Methods

### In Files

- lib/bio/appl/spidey/report.rb

### Parent

Object

### Methods

- ::new
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- #mrna
- #number_of_exons
- #number_of_splice_sites
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- #query_id
- #query_len
- #segmentpairs
- #strand
- #target_def
- #target_id
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### Files

- ChangeLog
- KNOWN_ISSUES.rdoc
- LEGAL
- README.rdoc
- README_DEV.rdoc
- RELEASE_NOTES.rdoc
- Changes-1.3.rdoc
- RELEASE_NOTES-1.4.0.rdoc
- RELEASE_NOTES-1.4.1.rdoc
- RELEASE_NOTES-1.4.2.rdoc

### Class/Module Index

Quicksearch

- Bio
- Bio::AAindex
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- Bio::Feature
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- Bio::FlatFileIndex::Indexer::Parser::PDBChemicalComponentParser
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- Bio::FlatFileIndex::Indexer::Parser::TemplateParser
- Bio::FlatFileIndex::NameSpaces
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- Bio::FlatFileIndex::Template::NameSpace
- Bio::GCG
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- Bio::GFF
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- Bio::GO
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- Bio::GenBank
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- Bio::GenPept::Locus
- Bio::Genscan
- Bio::Genscan::Report
- Bio::Genscan::Report::Exon
- Bio::Genscan::Report::Gene
- Bio::HGC
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- Bio::HMMER
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- Bio::HMMER::Report::Hit
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- Bio::Hinv
- Bio::Hinv::Acc2hit
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- Bio::Hinv::Hit2acc
- Bio::Hinv::HitCnt
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- Bio::UniProt
- BiorubyController
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- Hash
- Object
- String

No matching classes.

# Bio::Spidey::Report::Hit

Hit object of Spidey result. Similar to Bio::Blast::Report::Hit but lacks many methods.

### Public Class Methods

new(data, d0) click to toggle source

Creates a new Hit object. It is designed to be called internally from Bio::Spidey::Report::* classes. Users shall not call it directly.

    # File lib/bio/appl/spidey/report.rb, line 290
    def initialize(data, d0)
      @data = data
      @d0 = d0
    end

### Public Instance Methods

align() click to toggle source

Returns alignments. Returns an Array of arrays. This would be a Bio::Spidey specific method.

    # File lib/bio/appl/spidey/report.rb, line 465
    def align
      unless defined?(@align); parse_align; end
      @align
    end

complement?() click to toggle source

Returns true if the result reports 'Reverse complement'. Otherwise, return false or nil. This would be a Bio::Spidey specific method.

    # File lib/bio/appl/spidey/report.rb, line 330
    def complement?
      unless defined?(@complement); parse_strand; end
      @complement
    end

definition() click to toggle source
Alias for: target_def
each() click to toggle source

Iterates over each exon of the hit. Yields Bio::Spidey::Report::SegmentPair object.

    # File lib/bio/appl/spidey/report.rb, line 555
    def each(&x) #:yields: segmentpair
      exons.each(&x)
    end

exons() click to toggle source

Returns exons of the hit. Returns an array of Bio::Spidey::Report::SegmentPair object.

    # File lib/bio/appl/spidey/report.rb, line 437
    def exons
      unless defined?(@exons); parse_segmentpairs; end
      @exons
    end

Also aliased as: hsps
genomic() click to toggle source

Returns sequence informations of the 'Genomic'. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.

    # File lib/bio/appl/spidey/report.rb, line 373
    def genomic
      unless defined?(@genomic)
        @genomic = SeqDesc.parse(@d0.find { |x| /^Genomic\:/ =~ x })
      end
      @genomic
    end

hit_id() click to toggle source
Alias for: target_id
hsps() click to toggle source
Alias for: exons
introns() click to toggle source

Returns introns of the hit. Some of them would contain untranscribed regions. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

    # File lib/bio/appl/spidey/report.rb, line 447
    def introns
      unless defined?(@introns); parse_segmentpairs; end
      @introns
    end

len() click to toggle source
Alias for: target_len
missing_mrna_ends() click to toggle source

Returns missing mRNA ends of the hit.

    # File lib/bio/appl/spidey/report.rb, line 363
    def missing_mrna_ends
      unless defined?(@missing_mrna_ends)
        @missing_mrna_ends = field_fetch('Missing mRNA ends', @d0)
      end
      @missing_mrna_ends
    end

mrna() click to toggle source

Returns sequence informations of the mRNA. Returns a Bio::Spidey::Report::SeqDesc object. This would be a Bio::Spidey specific method.

    # File lib/bio/appl/spidey/report.rb, line 383
    def mrna
      unless defined?(@mrna)
        @mrna = SeqDesc.parse(@d0.find { |x| /^mRNA\:/ =~ x })
      end
      @mrna
    end

number_of_exons() click to toggle source

Returns number of exons in the hit.

    # File lib/bio/appl/spidey/report.rb, line 336
    def number_of_exons
      unless defined?(@number_of_exons)
        @number_of_exons = field_fetch('Number of exons', @d0).to_i
      end
      @number_of_exons
    end

number_of_splice_sites() click to toggle source

Returns number of splice sites of the hit.

    # File lib/bio/appl/spidey/report.rb, line 344
    def number_of_splice_sites
      unless defined?(@number_of_splice_sites)
        @number_of_splice_sites =
          field_fetch('Number of splice sites', @d0).to_i
      end
      @number_of_splice_sites
    end

percent_identity() click to toggle source

Returns overall percent identity of the hit.

    # File lib/bio/appl/spidey/report.rb, line 353
    def percent_identity
      unless defined?(@percent_identity)
        x = field_fetch('overall percent identity', @d0)
        @percent_identity =
          (/([\d\.]+)\s*\%/ =~ x.to_s) ? $1 : nil
      end
      @percent_identity
    end

query_def() click to toggle source

Definition of the mRNA (query). Same as Bio::Spidey::Report#query_def.

    # File lib/bio/appl/spidey/report.rb, line 536
    def query_def;  mrna.definition; end

query_id() click to toggle source

Identifier of the mRNA (query). Same as Bio::Spidey::Report#query_id.

    # File lib/bio/appl/spidey/report.rb, line 532
    def query_id;   mrna.entry_id;   end

query_len() click to toggle source

Length of the mRNA (query) sequence. Same as Bio::Spidey::Report#query_len.

    # File lib/bio/appl/spidey/report.rb, line 528
    def query_len;  mrna.len;        end

segmentpairs() click to toggle source

Returns segment pairs (exons and introns) of the hit. Each segment pair is a Bio::Spidey::Report::SegmentPair object. Returns an array of Bio::Spidey::Report::SegmentPair objects. (Note that intron data is not always available according to run-time options of the program.)

    # File lib/bio/appl/spidey/report.rb, line 457
    def segmentpairs
      unless defined?(@segmentparis); parse_segmentpairs; end
      @segmentpairs
    end

strand() click to toggle source

Returns strand information of the hit. Returns 'plus', 'minus', or nil. This would be a Bio::Spidey specific method.

    # File lib/bio/appl/spidey/report.rb, line 322
    def strand
      unless defined?(@strand); parse_strand; end
      @strand
    end

target_def() click to toggle source

Definition of the genomic (target) sequence.

    # File lib/bio/appl/spidey/report.rb, line 545
    def target_def; genomic.definition; end

Also aliased as: definition
target_id() click to toggle source

Identifier of the genomic (target) sequence.

    # File lib/bio/appl/spidey/report.rb, line 542
    def target_id;  genomic.entry_id;   end

Also aliased as: hit_id
target_len() click to toggle source

The genomic (target) sequence length.

    # File lib/bio/appl/spidey/report.rb, line 539
    def target_len; genomic.len;        end

Also aliased as: len

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