class Nucleotide::Translate
Public Class Methods
new(table)
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Table can be either an id (integer) or a Biolib::Emboss TrnTable
# File lib/bigbio/sequence/translate.rb, line 13 def initialize table table = 0 if table == nil if table.kind_of? Numeric @trn_table = Bio::Big::TranslationAdapter.translation_table(table) else @trn_table = table end end
Public Instance Methods
aa_6_frames(seq)
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Return all six reading frames as an Array - ordered as frames [1,2,3,-1,-2,-3] with as tuples [frame, AAsequence].
Note that the nucleotide sequence does not get modified.
# File lib/bigbio/sequence/translate.rb, line 27 def aa_6_frames seq res = [] # remove white space seq = seq.gsub(/\s/,'') [1,2,3,-1,-2,-3].each do | frame | aa = Bio::Big::TranslationAdapter.translate(@trn_table,frame,seq) res.push({:frame => frame, :sequence => aa}) end res end
aa_forward_frames(seq)
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Return all forward reading frames as an Array - ordered as frames [1,2,3] with as tuples [frame, AAsequence]
# File lib/bigbio/sequence/translate.rb, line 40 def aa_forward_frames seq res = [] # remove white space seq = seq.gsub(/\s/,'') [1,2,3].each do | frame | aa = Bio::Big::TranslationAdapter.translate(@trn_table,frame,seq) res.push({:frame => frame, :sequence => aa}) end res end