[BioPython] codons and complements

[Jeffrey Chang]

> Next question should we use 'clever' translation ? (or greedy translation?)
> Synonymous codons, like CTA, CTT, CTG and gives Leucine(L). Should CTN
> (maybe from a sequencing error) recognize the codon family and translate
> CIN to L ? 

Encoding "wobble" into the translator is an interesting idea.

I believe Andrew's scheme can currently handle this.

(stolen from Andrew's MarkMissingCodon example)

(sequence table information from NCBI:
ftp://ncbi.nlm.nih.gov/entrez/misc/data/seqcode.prt
)

class MarkAmbiguousCodon:
  ambiguous_table = {"B" : ['G', 'T', 'C'],
                     "D" : ['G', 'A', 'T'],
                     ...}

  def __init__(self, codon_table):
    self.data = codon_table
  def __getitem__(self, key):
    try:
      return self.data[key]
    except KeyError:
      # Generate a list of all the possible codon resolutions.            
      # Check to make sure that they all encode the same amino acid.
      #   What happens if they don't?
      
      
class MarkAmbiguousTable:
  def __init__(self, codon_table):
    self.codon_table = MarkAmbiguousCodon(codon_table)
    self.output_seq_constructor = ProteinSeq

translate(seq, MarkAmbiguousTable(seq.codon_table))

Jeff