### Home Classes Methods

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

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### Files

- KNOWN_ISSUES.rdoc
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- RELEASE_NOTES-1.4.1.rdoc
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No matching classes.

# Bio::Spidey::Report::SegmentPair

Sequence segment pair of Spidey result. Similar to Bio::Blast::Report::Hsp but lacks many methods. For mRNA-genome mapping programs, unlike other homology search programs, the class is used not only for exons but also for introns. (Note that intron data would not be available according to run-time options of the program.)

### Attributes

aaseqline[R]

Returns amino acide sequence in alignment. Returns String, because white spaces is also important. Returns nil if no alignment data are available.

align_len[R]

Returns alignment length of the segment pair. Returns nil if no alignment data are available.

gaps[R]

Returns gaps.

genomic[R]

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

midline[R]

Returns the middle line of the alignment of the segment pair. Returns nil if no alignment data are available.

mismatch_count[R]

Returns mismatches.

mismatches[R]

Returns mismatches.

mrna[R]

Returns segment informations of the 'mRNA'. Returns a Bio::Spidey::Report::Segment object. This would be a Bio::Spidey specific method.

percent_identity[R]

Returns percent identity of the segment pair.

splice_site[R]

Returns splice site information. Returns a hash which contains :d and :a for keys and 0, 1, or nil for values. This would be a Bio::Spidey specific methods.

### Public Class Methods

new(genomic, mrna, midline, aaseqline, percent_identity, mismatches, gaps, splice_site, align_len) click to toggle source

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

    # File lib/bio/appl/spidey/report.rb, line 125
    def initialize(genomic, mrna, midline, aaseqline,
                   percent_identity, mismatches, gaps, splice_site,
                   align_len)
      @genomic   = genomic
      @mrna      = mrna
      @midline   = midline
      @aaseqline = aaseqline
      @percent_identity = percent_identity
      @mismaches        = mismatches
      @gaps             = gaps
      @splice_site      = splice_site
      @align_len        = align_len
    end

new_intron(from, to, strand, aln) click to toggle source

Creates a new SegmentPair object when the segment pair is an intron. 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 182
    def self.new_intron(from, to, strand, aln)
      genomic   = Segment.new(from, to, strand, aln[0])
      mrna      = Segment.new(nil, nil, nil,    aln[2])
      midline   = aln[1]
      aaseqline = aln[3]
      self.new(genomic, mrna, midline, aaseqline,
               nil, nil, nil, nil, nil)
    end

parse(str, strand, complement, aln) click to toggle source

Parses a piece of Spidey result text and creates a new SegmentPair 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 196
    def self.parse(str, strand, complement, aln)
      /\AExon\s*\d+(\(\-\))?\:\s*(\d+)\-(\d+)\s*\(gen\)\s+(\d+)\-(\d+)\s*\(mRNA\)\s+id\s*([\d\.]+)\s*\%\s+mismatches\s+(\d+)\s+gaps\s+(\d+)\s+splice site\s*\(d +a\)\s*\:\s*(\d+)\s+(\d+)/ =~ str
      if strand == 'minus' then
        genomic = Segment.new($3, $2, strand, aln[0])
      else
        genomic = Segment.new($2, $3, 'plus', aln[0])
      end
      if complement then
        mrna    = Segment.new($4, $5, 'minus', aln[2])
      else
        mrna    = Segment.new($4, $5, 'plus',  aln[2])
      end
      percent_identity = $6
      mismatches = ($7 ? $7.to_i : nil)
      gaps = ($8 ? $8.to_i : nil)
      splice_site = {
        :d => ($9  ? $9.to_i  : nil),
        :a => ($10 ? $10.to_i : nil)
      }
      midline   = aln[1]
      aaseqline = aln[3]
      self.new(genomic, mrna, midline, aaseqline,
               percent_identity, mismatches, gaps, splice_site,
               (midline ? midline.length : nil))
    end

### Public Instance Methods

hit_from() click to toggle source

Returns start position of the genomic (target, hit) (the first position is 1).

    # File lib/bio/appl/spidey/report.rb, line 243
    def hit_from;     @genomic.from;    end

hit_strand() click to toggle source

Returns strand information of the genomic (target, hit). Returns 'plus', 'minus', or nil.

    # File lib/bio/appl/spidey/report.rb, line 254
    def hit_strand;   @genomic.strand;  end

hit_to() click to toggle source

Returns end position (including its position) of the genomic (target, hit).

    # File lib/bio/appl/spidey/report.rb, line 247
    def hit_to;       @genomic.to;      end

hseq() click to toggle source

Returns the sequence (with gaps) of the genomic (target, hit).

    # File lib/bio/appl/spidey/report.rb, line 250
    def hseq;         @genomic.seq;     end

qseq() click to toggle source

Returns the sequence (with gaps) of the mRNA (query).

    # File lib/bio/appl/spidey/report.rb, line 235
    def qseq;         @mrna.seq;        end

query_from() click to toggle source

Returns start position of the mRNA (query) (the first position is 1).

    # File lib/bio/appl/spidey/report.rb, line 229
    def query_from;   @mrna.from;       end

query_strand() click to toggle source

Returns strand information of the mRNA (query). Returns 'plus', 'minus', or nil.

    # File lib/bio/appl/spidey/report.rb, line 239
    def query_strand; @mrna.strand;     end

query_to() click to toggle source

Returns end position (including its position) of the mRNA (query).

    # File lib/bio/appl/spidey/report.rb, line 232
    def query_to;     @mrna.to;         end

[Validate]

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