class FastaPairedRecord
Attributes
aa[R]
nt[R]
Public Class Methods
new(nt, aa)
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# 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()
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# File lib/bigbio/db/fasta/fastarecord.rb, line 42 def id @aa.id end