Class: BlastHit

Inherits:
Object
  • Object
show all
Defined in:
lib/rocker/blasthit.rb

Overview

Author:

  • Luis M. Rodriguez-R <lmrodriguezr at gmail dot com>

  • Luis (Coto) Orellana

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(ln, aln = nil) ⇒ BlastHit

Initialize from BLAST using new(ln,aln), initialize from TABLE using new(ln)



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# File 'lib/rocker/blasthit.rb', line 11

def initialize(ln, aln=nil)
   l = ln.chomp.split(/\t/)
   if aln.nil?
	 @sbj	= l[0]
	 @sfrom	= l[1].to_i
	 @sto	= l[2].to_i
	 @bits	= l[3].to_f
	 @istrue = l[4]=='1'
	 @midpoint = l[5].to_i
   else
	 s = aln.seq(l[1])
	 return nil if s.nil?
	 @sbj	= s.id
	 a	= s.pos2col(l[8].to_i)
	 b 	= s.pos2col(l[9].to_i)
	 @sfrom	= [a,b].min
	 @sto	= [a,b].max
	 @bits	= l[11].to_f
	 @istrue = ! /@%/.match(l[0]).nil?
	 @midpoint = s.pos2col(((l[8].to_f+l[9].to_f)/2).ceil)
   end
end

Instance Attribute Details

#bits ⇒ Object (readonly)

Returns the value of attribute bits.



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# File 'lib/rocker/blasthit.rb', line 9

def bits
  @bits
end

#istrue ⇒ Object (readonly)

Returns the value of attribute istrue.



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# File 'lib/rocker/blasthit.rb', line 9

def istrue
  @istrue
end

#midpoint ⇒ Object (readonly)

Returns the value of attribute midpoint.



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# File 'lib/rocker/blasthit.rb', line 9

def midpoint
  @midpoint
end

#sbj ⇒ Object (readonly)

Returns the value of attribute sbj.



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# File 'lib/rocker/blasthit.rb', line 9

def sbj
  @sbj
end

#sfrom ⇒ Object (readonly)

Returns the value of attribute sfrom.



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# File 'lib/rocker/blasthit.rb', line 9

def sfrom
  @sfrom
end

#sto ⇒ Object (readonly)

Returns the value of attribute sto.



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# File 'lib/rocker/blasthit.rb', line 9

def sto
  @sto
end

Instance Method Details

#to_s ⇒ Object 



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# File 'lib/rocker/blasthit.rb', line 33

def to_s
   self.sbj.nil? ? "" :
	 [self.sbj, self.sfrom.to_s, self.sto.to_s, self.bits.to_s,
  self.istrue ? '1' : '0', self.midpoint].join("\t") + "\n"
end