Benjamin-Lee / Benjamin-Lee/CodonAdaptationIndex

absent amino acids

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Description

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}

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