absent amino acids

[lalalagartija]

Hi,

Thanks for this very convenient package. I would like to point out a problem with the existing rscu calculation that is that even absent amino acids get values. There should be an option to return missing values when amino acids are absent in order to avoid sporadious comparisons.

As an example :
the command:
RSCU(['ATGACCAGCAGCAGC'],genetic_code=1)
returns:
{'TTT': 1.0, 'TTC': 1.0, 'TTA': 1.0, 'TTG': 1.0, 'TCT': 0.5454545454545455, 'TCC': 0.5454545454545455, 'TCA': 0.5454545454545455, 'TCG': 0.5454545454545455, 'TAT': 1.0, 'TAC': 1.0, 'TGT': 1.0, 'TGC': 1.0, 'TGG': 1.0, 'CTT': 1.0, 'CTC': 1.0, 'CTA': 1.0, 'CTG': 1.0, 'CCT': 1.0, 'CCC': 1.0, 'CCA': 1.0, 'CCG': 1.0, 'CAT': 1.0, 'CAC': 1.0, 'CAA': 1.0, 'CAG': 1.0, 'CGT': 1.0, 'CGC': 1.0, 'CGA': 1.0, 'CGG': 1.0, 'ATT': 1.0, 'ATC': 1.0, 'ATA': 1.0, 'ATG': 1.0, 'ACT': 0.8, 'ACC': 1.6, 'ACA': 0.8, 'ACG': 0.8, 'AAT': 1.0, 'AAC': 1.0, 'AAA': 1.0, 'AAG': 1.0, 'AGT': 0.5454545454545455, 'AGC': 3.272727272727273, 'AGA': 1.0, 'AGG': 1.0, 'GTT': 1.0, 'GTC': 1.0, 'GTA': 1.0, 'GTG': 1.0, 'GCT': 1.0, 'GCC': 1.0, 'GCA': 1.0, 'GCG': 1.0, 'GAT': 1.0, 'GAC': 1.0, 'GAA': 1.0, 'GAG': 1.0, 'GGT': 1.0, 'GGC': 1.0, 'GGA': 1.0, 'GGG': 1.0}

[lalalagartija]

I have changed the function RSCU to suit my needs in this way:
by adding
import numpy as np

then
` # "if a certain codon is never used in the reference set... assign [its
# count] a value of 0.5" (page 1285)
never_used=[]
for codon in ct.unambiguous_dna_by_id[genetic_code].forward_table:
if counts[codon] == 0:
counts[codon] = 0.5
never_used.append(codon)

# determine the synonymous codons for the genetic code
synonymous_codons = _synonymous_codons[genetic_code]

# hold the result as it is being calulated
result = {}

# calculate RSCU values
for codon in ct.unambiguous_dna_by_id[genetic_code].forward_table:
    missingaacount=len([x for x in synonymous_codons[codon] if x in never_used])
    if missingaacount == len(synonymous_codons[codon]) : 
        result[codon]=np.nan
    else: 
        result[codon] = counts[codon] / (
            (len(synonymous_codons[codon]) ** -1)
            * (sum((counts[_codon] for _codon in synonymous_codons[codon])))
            * 
            * `