class ORF
Attributes
aa[R]
descr[R]
frame[R]
id[R]
nt[R]
Public Class Methods
new(num, type, id, descr, nt, frame, start, aa)
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# File lib/bigbio/sequence/predictorf.rb, line 42 def initialize num, type, id, descr, nt, frame, start, aa @id = id.to_s + '_' + (num + 1).to_s # ---- adjust start to match frame start += frame.abs-1 # ---- stop should not go beyond sequence stop = start + aa.size * 3 if stop > nt.size stop = nt.size end # ---- if frame < 0 it should reverse complement if frame < 0 nt = Bio::Sequence::NA.new(nt).reverse_complement.to_s.upcase end # p [start, stop, stop-start] # p nt fr = frame.to_s fr = '+'+fr if frame > 0 @descr = "[#{type} #{fr} #{start} - #{stop}; #{stop-start}/#{nt.size}] " + descr @nt = ORFnucleotides.new(nt, start, stop) @frame = frame @aa = ORFaminoacids.new(aa) end
Public Instance Methods
<=>(other)
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# File lib/bigbio/sequence/predictorf.rb, line 65 def <=> other if frame == other.frame nt.seq <=> other.nt.seq else frame <=> other.frame end end
to_fastarec()
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# File lib/bigbio/sequence/predictorf.rb, line 73 def to_fastarec aa = FastaRecord.new(@id,@descr,@aa.seq) nt = FastaRecord.new(@id,@descr,@nt.seq) FastaPairedRecord.new(nt,aa) end