class BlastHit
@author Luis M. Rodriguez-R <lmrodriguezr at gmail dot com> @author Luis (Coto) Orellana @license artistic license 2.0 @update Sep-06-2015
Attributes
bits[R]
isfalse[R]
istrue[R]
midpoint[R]
qry[R]
sbj[R]
sfrom[R]
sto[R]
Public Class Methods
new(ln, aln=nil)
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Initialize from BLAST using new(ln,aln), initialize from TABLE using new(ln)
# File lib/rocker/blasthit.rb, line 12 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' @istrue = l[4]=='-1' @midpoint = l[5].to_i else @qry = l[0] 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? @isfalse = ! /@\$/.match(l[0]).nil? @midpoint = s.pos2col(((l[8].to_f+l[9].to_f)/2).ceil) end end
Public Instance Methods
to_s()
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# File lib/rocker/blasthit.rb, line 37 def to_s self.sbj.nil? ? "" : [sbj, sfrom.to_s, sto.to_s, bits.to_s, istrue ? "1" : (isfalse ? "-1" : "0"), midpoint].join("\t") + "\n" end