Class: BlastHit

Inherits:
Object
  • Object
show all
Defined in:
lib/scbi_blast/blast_hit.rb

Overview

Class for a Blast Hit (a concordance between a query and a subject)

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(q_beg, q_end, s_beg, s_end) ⇒ BlastHit

initializes a new hit



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# File 'lib/scbi_blast/blast_hit.rb', line 27

def initialize(q_beg,q_end,s_beg,s_end)
  set_limits(q_beg,q_end,s_beg,s_end)
end

Instance Attribute Details

#acc ⇒ Object

Returns the value of attribute acc.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def acc
  @acc
end

#align_len ⇒ Object

Returns the value of attribute align_len.



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# File 'lib/scbi_blast/blast_hit.rb', line 190

def align_len
  @align_len
end

#bit_score ⇒ Object

Returns the value of attribute bit_score.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def bit_score
  @bit_score
end

#definition ⇒ Object

Returns the value of attribute definition.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def definition
  @definition
end

#e_val ⇒ Object

Returns the value of attribute e_val.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def e_val
  @e_val
end

#full_subject_length ⇒ Object

Returns the value of attribute full_subject_length.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def full_subject_length
  @full_subject_length
end

#gaps ⇒ Object

Returns the value of attribute gaps.



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# File 'lib/scbi_blast/blast_hit.rb', line 190

def gaps
  @gaps
end

#ident ⇒ Object

Returns the value of attribute ident.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def ident
  @ident
end

#mismatches ⇒ Object

Returns the value of attribute mismatches.



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# File 'lib/scbi_blast/blast_hit.rb', line 190

def mismatches
  @mismatches
end

#q_beg ⇒ Object

readers and accessor for properties



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# File 'lib/scbi_blast/blast_hit.rb', line 189

def q_beg
  @q_beg
end

#q_end ⇒ Object

readers and accessor for properties



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# File 'lib/scbi_blast/blast_hit.rb', line 189

def q_end
  @q_end
end

#q_frame ⇒ Object

Returns the value of attribute q_frame.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def q_frame
  @q_frame
end

#q_len ⇒ Object

Returns the value of attribute q_len.



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# File 'lib/scbi_blast/blast_hit.rb', line 193

def q_len
  @q_len
end

#q_seq ⇒ Object

Returns the value of attribute q_seq.



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# File 'lib/scbi_blast/blast_hit.rb', line 193

def q_seq
  @q_seq
end

#reversed ⇒ Object

Returns the value of attribute reversed.



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# File 'lib/scbi_blast/blast_hit.rb', line 191

def reversed
  @reversed
end

#s_beg ⇒ Object

readers and accessor for properties



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# File 'lib/scbi_blast/blast_hit.rb', line 189

def s_beg
  @s_beg
end

#s_end ⇒ Object

readers and accessor for properties



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# File 'lib/scbi_blast/blast_hit.rb', line 189

def s_end
  @s_end
end

#s_frame ⇒ Object

Returns the value of attribute s_frame.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def s_frame
  @s_frame
end

#s_len ⇒ Object

Returns the value of attribute s_len.



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# File 'lib/scbi_blast/blast_hit.rb', line 193

def s_len
  @s_len
end

#s_seq ⇒ Object

Returns the value of attribute s_seq.



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# File 'lib/scbi_blast/blast_hit.rb', line 193

def s_seq
  @s_seq
end

#score ⇒ Object

Returns the value of attribute score.



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# File 'lib/scbi_blast/blast_hit.rb', line 192

def score
  @score
end

#subject_id ⇒ Object

Returns the value of attribute subject_id.



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# File 'lib/scbi_blast/blast_hit.rb', line 190

def subject_id
  @subject_id
end

Instance Method Details

#compare?(hit) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_blast/blast_hit.rb', line 147

def compare?(hit)
  res=true
  
  res &&=( @q_beg==hit.q_beg)
  res &&=( @q_end==hit.q_end)
  res &&=( @s_beg==hit.s_beg)
  res &&=( @s_end==hit.s_end)
  
  res &&=( @subject_id==hit.subject_id)
  res &&=( @align_len==hit.align_len)
  res &&=( @gaps==hit.gaps)
  res &&=( @mismatches==hit.mismatches)
  
  
  res &&=( @reversed==hit.reversed)
  res &&=( @score==hit.score)
  res &&=( @acc==hit.acc)
  res &&=( @definition==hit.definition)
  
  
  res &&=( @q_frame==hit.q_frame)
  res &&=( @s_frame==hit.s_frame)
  res &&=( @full_subject_length==hit.full_subject_length)
  res &&=( @ident==hit.ident)
  
  
  res &&=( @e_val==hit.e_val)
  res &&=( @bit_score==hit.bit_score)
  res &&=( @q_seq==hit.q_seq)
  res &&=( @s_seq==hit.s_seq)
  
  if !res 
    puts "Hits not equal:"
    puts inspect
    puts "="*20
    puts hit.inspect
  end
  
  return res
end

#get_subject ⇒ Object 



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# File 'lib/scbi_blast/blast_hit.rb', line 135

def get_subject
  return @subject_id
end

#inspect ⇒ Object

puts all hit info on a string



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# File 'lib/scbi_blast/blast_hit.rb', line 128

def inspect
  res =  "Hit: #{@subject_id.ljust(10)} #{@ident.to_s.rjust(4)} #{@align_len.to_s.rjust(2)} #{@mismatches.to_s.rjust(2)} #{@gaps.to_s.rjust(2)} #{@q_beg.to_s.rjust(5)} #{@q_end.to_s.rjust(5)} #{@s_beg.to_s.rjust(5)} #{@s_end.to_s.rjust(5)} #{@e_val.to_s.rjust(5)}  #{@bit_score.to_s.rjust(5)} #{@reversed.to_s.rjust(5)}"
  res += " #{@score.to_s.rjust(5)} #{@acc.ljust(10)} #{@definition.ljust(10)} #{@q_frame.to_s.rjust(2)} #{@s_frame.to_s.rjust(2)} #{@full_subject_length.to_s.rjust(5)} #{@q_seq}.#{@s_seq}.#{@q_len}.#{@s_len}"

  return res
end

#query_overlaps?(hit, threshold = 0) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'lib/scbi_blast/blast_hit.rb', line 139

def query_overlaps?(hit,threshold=0)
  return ((@q_beg<=(hit.q_end+threshold)) and ((@q_end+threshold)>=hit.q_beg))
end

#set_limits(q_beg, q_end, s_beg, s_end) ⇒ Object 



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# File 'lib/scbi_blast/blast_hit.rb', line 31

def set_limits(q_beg,q_end,s_beg,s_end)
  # puts "Set limits #{[q_beg,q_end,s_beg,s_end].join(',')}"
  @q_beg = q_beg.to_i-1  #blast indexes are 1 based
  @q_end = q_end.to_i-1
  @s_beg = s_beg.to_i-1
  @s_end = s_end.to_i-1
  # puts "Set limits2 #{[@q_beg,@q_end,@s_beg,@s_end].join(',')}"
  
  @s_len=0
  @q_len=0

  @reversed = false

  # TODO -Reversed should be taken from q_frame and s_frame instead of s_end. In proteins comes from q_frame. In nt from s_frames.

  # check if reversed
  if @s_beg > @s_end
    @s_beg = s_end.to_i-1
    @s_end = s_beg.to_i-1
    @reversed = true
  end
  # puts "Set limits3 #{[@q_beg,@q_end,@s_beg,@s_end].join(',')}"
  # puts "Set limits4 #{[q_beg,q_end,s_beg,s_end].join(',')}"
  
end

#size ⇒ Object 



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# File 'lib/scbi_blast/blast_hit.rb', line 143

def size
  return (@q_end-@q_beg+1)
end