class FastaPairedRecord

Attributes

aa[R]
nt[R]

Public Class Methods

new(nt, aa) click to toggle source
# File lib/bigbio/db/fasta/fastarecord.rb, line 19
def initialize nt, aa
  @nt = nt
  @aa = aa
  raise "ID error NT #{nt.id} not matching AA #{aa.id}" if nt.id != aa.id
  if nt.seq.size == aa.seq.size*3-1
    # account for EMBOSS cleverness
    nt.seq.chop!
    nt.seq.chop!
    aa.seq.chop!
  end
  if nt.seq.size == aa.seq.size*3-2
    # account for EMBOSS cleverness
    nt.seq.chop!
    aa.seq.chop!
  end
  if nt.seq.size == aa.seq.size*3-3
    aa.seq.chop!
  end
  nt_size = nt.seq.size
  expected_size = aa.seq.size*3
  # raise "Sequence size mismatch for #{nt.id} <nt:#{nt.seq.size} != #{aa.seq.size*3} (aa:#{aa.seq.size}*3)>" if expected_size - 3 > nt_size and  nt_size > expected_size + 3
end

Public Instance Methods

id() click to toggle source
# File lib/bigbio/db/fasta/fastarecord.rb, line 42
def id
  @aa.id
end