Class: Hsp

Inherits:

Object

• Object
• Hsp

show all

Defined in:

lib/genevalidator/hsp.rb

Instance Attribute Summary (collapse)

• - (Object) align_len

  Returns the value of attribute align_len.

• - (Object) bit_score

  positive (mis)matches with +, mismatches and gaps are with space.

• - (Object) gaps

  Returns the value of attribute gaps.

• - (Object) hit_alignment

  Returns the value of attribute hit_alignment.

• - (Object) hit_from

  references from the unaligned hit sequence.

• - (Object) hit_to

  Returns the value of attribute hit_to.

• - (Object) hsp_evalue

  Returns the value of attribute hsp_evalue.

• - (Object) hsp_score

  Returns the value of attribute hsp_score.

• - (Object) identity

  number of conserved residues.

• - (Object) match_query_from

  references from the unaligned query sequence.

• - (Object) match_query_to

  Returns the value of attribute match_query_to.

• - (Object) middles

  conserved residues are with letters,.

• - (Object) pidentity

  percentage of identical matches.

• - (Object) positive

  positive score for the (mis)match.

• - (Object) query_alignment

  Returns the value of attribute query_alignment.

• - (Object) query_reading_frame

  Returns the value of attribute query_reading_frame.

Instance Method Summary (collapse)

• - (Object) init_tabular_attribute(column, value, type = :protein)

  Initializes the corresponding attribute of the hsp with respect to the column name of the tabular blast output Params: column: String with column name value: Value of the column type: type of the sequences: :nucleotide or :protein.

• - (Hsp) initialize constructor

  A new instance of Hsp.

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# File 'lib/genevalidator/hsp.rb', line 25

def initialize
  query_alignment = nil
  hit_alignment = nil
end

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# File 'lib/genevalidator/hsp.rb', line 23

def align_len
  @align_len
end

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# File 'lib/genevalidator/hsp.rb', line 16

def bit_score
  @bit_score
end

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# File 'lib/genevalidator/hsp.rb', line 22

def gaps
  @gaps
end

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# File 'lib/genevalidator/hsp.rb', line 11

def hit_alignment
  @hit_alignment
end

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# File 'lib/genevalidator/hsp.rb', line 6

def hit_from
  @hit_from
end

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# File 'lib/genevalidator/hsp.rb', line 7

def hit_to
  @hit_to
end

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# File 'lib/genevalidator/hsp.rb', line 18

def hsp_evalue
  @hsp_evalue
end

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# File 'lib/genevalidator/hsp.rb', line 17

def hsp_score
  @hsp_score
end

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# File 'lib/genevalidator/hsp.rb', line 19

def identity
  @identity
end

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# File 'lib/genevalidator/hsp.rb', line 8

def match_query_from
  @match_query_from
end

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# File 'lib/genevalidator/hsp.rb', line 9

def match_query_to
  @match_query_to
end

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# File 'lib/genevalidator/hsp.rb', line 13

def middles
  @middles
end

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# File 'lib/genevalidator/hsp.rb', line 20

def pidentity
  @pidentity
end

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# File 'lib/genevalidator/hsp.rb', line 21

def positive
  @positive
end

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# File 'lib/genevalidator/hsp.rb', line 12

def query_alignment
  @query_alignment
end

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# File 'lib/genevalidator/hsp.rb', line 10

def query_reading_frame
  @query_reading_frame
end

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# File 'lib/genevalidator/hsp.rb', line 37

def init_tabular_attribute(column, value, type=:protein)
  case column
    when "qstart"
      if type == :nucleotide
        @match_query_from = (value.to_i/3)+1
      else
        @match_query_from = value.to_i
      end
    when "qend"
      if type == :nucleotide
        @match_query_to = (value.to_i/3) + 1
      else
        @match_query_to = value.to_i
      end
    when "qframe"
      @query_reading_frame = value.to_i
    when "sstart"
      @hit_from = value.to_i
    when "send"
      @hit_to = value.to_i
    when "qseq"
      @query_alignment = value
      seq_type = BlastUtils.guess_sequence_type(value)
      if seq_type != nil and seq_type != :protein
        raise SequenceTypeError
      end
    when "sseq"
      @hit_alignment = value
      seq_type = BlastUtils.guess_sequence_type(value)
      if seq_type != nil and seq_type != :protein
        raise SequenceTypeError
      end
    when "length"
      @align_len = value.to_i
    when "pident"
      @pidentity = value.to_f
    when "evalue"
      @hsp_evalue = value.to_f
  end
end