Class: GeneValidator::Hsp

Inherits:
Object
  • Object
show all
Extended by:
Forwardable
Defined in:
lib/genevalidator/hsp.rb

Overview

A class that initialises the BLAST tabular attributes

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(input = {}) ⇒ Hsp

Returns a new instance of Hsp.



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# File 'lib/genevalidator/hsp.rb', line 31

def initialize(input = {})
  @query_alignment = nil
  @hit_alignment   = nil
  init_xml_attributes(input[:xml_input]) if input[:xml_input]
  init_tabular_attribute(input[:tabular_input]) if input[:tabular_input]
end

Instance Attribute Details

#align_len ⇒ Object

Returns the value of attribute align_len.



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# File 'lib/genevalidator/hsp.rb', line 29

def align_len
  @align_len
end

#bit_score ⇒ Object

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



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

def bit_score
  @bit_score
end

#gaps ⇒ Object

Returns the value of attribute gaps.



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# File 'lib/genevalidator/hsp.rb', line 28

def gaps
  @gaps
end

#hit_alignment ⇒ Object

Returns the value of attribute hit_alignment.



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

def hit_alignment
  @hit_alignment
end

#hit_from ⇒ Object

ref. from the unaligned hit sequence



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

def hit_from
  @hit_from
end

#hit_to ⇒ Object

Returns the value of attribute hit_to.



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

def hit_to
  @hit_to
end

#hsp_evalue ⇒ Object

Returns the value of attribute hsp_evalue.



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# File 'lib/genevalidator/hsp.rb', line 24

def hsp_evalue
  @hsp_evalue
end

#hsp_score ⇒ Object

Returns the value of attribute hsp_score.



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

def hsp_score
  @hsp_score
end

#identity ⇒ Object

number of conserved residues



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

def identity
  @identity
end

#match_query_from ⇒ Object

ref. from the unaligned query sequence



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# File 'lib/genevalidator/hsp.rb', line 14

def match_query_from
  @match_query_from
end

#match_query_to ⇒ Object

Returns the value of attribute match_query_to.



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# File 'lib/genevalidator/hsp.rb', line 15

def match_query_to
  @match_query_to
end

#middles ⇒ Object

conserved residues are with letters,



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

def middles
  @middles
end

#pidentity ⇒ Object

percentage of identical matches



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# File 'lib/genevalidator/hsp.rb', line 26

def pidentity
  @pidentity
end

#positive ⇒ Object

positive score for the (mis)match



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# File 'lib/genevalidator/hsp.rb', line 27

def positive
  @positive
end

#query_alignment ⇒ Object

Returns the value of attribute query_alignment.



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

def query_alignment
  @query_alignment
end

#query_reading_frame ⇒ Object

Returns the value of attribute query_reading_frame.



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

def query_reading_frame
  @query_reading_frame
end

Instance Method Details

#assert_seq_type(query) ⇒ Object 



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# File 'lib/genevalidator/hsp.rb', line 79

def assert_seq_type(query)
  seq_type = BlastUtils.guess_sequence_type(query)
  raise SequenceTypeError if seq_type != :protein
rescue SequenceTypeError => e
  warn e
  exit 1
end

#init_tabular_attribute(hash) ⇒ Object

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



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# File 'lib/genevalidator/hsp.rb', line 63

def init_tabular_attribute(hash)
  @match_query_from    = hash['qstart'].to_i if hash['qstart']
  @match_query_to      = hash['qend'].to_i if hash['qend']
  @query_reading_frame = hash['qframe'].to_i if hash['qframe']
  @hit_from            = hash['sstart'].to_i if hash['sstart']
  @hit_to              = hash['send'].to_i if hash['send']
  @query_alignment     = hash['qseq'] if hash['qseq']
  @hit_alignment       = hash['sseq'] if hash['sseq']
  @align_len           = hash['length'].to_i if hash['length']
  @pidentity           = hash['pident'].to_f if hash['pident']
  @identity            = hash['nident'].to_f if hash['nident']
  @hsp_evalue          = hash['evalue'].to_f if hash['evalue']
  assert_seq_type(@query_alignment) if hash['sseq']
  assert_seq_type(@hit_alignment) if hash['sseq']
end

#init_xml_attributes(hsp) ⇒ Object 



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# File 'lib/genevalidator/hsp.rb', line 38

def init_xml_attributes(hsp)
  @match_query_from    = hsp.query_from.to_i
  @match_query_to      = hsp.query_to.to_i
  @query_reading_frame = hsp.query_frame.to_i
  @hit_from            = hsp.hit_from.to_i
  @hit_to              = hsp.hit_to.to_i
  @query_alignment     = hsp.qseq.to_s
  @hit_alignment       = hsp.hseq.to_s
  @align_len           = hsp.align_len.to_i
  @pidentity           = (100 * hsp.identity / hsp.align_len.to_f).round(2)
  @identity            = hsp.identity.to_i
  @hsp_evalue          = format('%.0e', hsp.evalue)
  assert_seq_type(@hit_alignment) if @hit_alignment
  assert_seq_type(@query_alignment) if @query_alignment
  return unless config[:type] == :nucleotide
  @match_query_from = (@match_query_from / 3) + 1
  @match_query_to   = (@match_query_to / 3) + 1
end