Class constant dictionary in Python

Question

I'm building a module that has a class variable dictionary:

class CodonUsageTable:
        CODON_DICT={'TTT': 0, 'TTC': 0, 'TTA': 0, 'TTG': 0, 'CTT': 0,
        'CTC': 0, 'CTA': 0, 'CTG': 0, 'ATT': 0, 'ATC': 0,
        'ATA': 0, 'ATG': 0, 'GTT': 0, 'GTC': 0, 'GTA': 0,
        'GTG': 0, 'TAT': 0, 'TAC': 0, 'TAA': 0, 'TAG': 0,
        'CAT': 0, 'CAC': 0, 'CAA': 0, 'CAG': 0, 'AAT': 0,
        'AAC': 0, 'AAA': 0, 'AAG': 0, 'GAT': 0, 'GAC': 0,
        'GAA': 0, 'GAG': 0, 'TCT': 0, 'TCC': 0, 'TCA': 0,
        'TCG': 0, 'CCT': 0, 'CCC': 0, 'CCA': 0, 'CCG': 0,
        'ACT': 0, 'ACC': 0, 'ACA': 0, 'ACG': 0, 'GCT': 0,
        'GCC': 0, 'GCA': 0, 'GCG': 0, 'TGT': 0, 'TGC': 0,
        'TGA': 0, 'TGG': 0, 'CGT': 0, 'CGC': 0, 'CGA': 0,
        'CGG': 0, 'AGT': 0, 'AGC': 0, 'AGA': 0, 'AGG': 0,

#Other code

        def __init__(self,seqobj):
                '''Creates codon table for a given Bio.seq object.i
                The only argument is Bio.Seq object with DNA
                Currently assumes seq to be DNA, RNA support to be added later'''
                dnaseq=str(seqobj)
                self.usage_table=CodonUsageTable.CODON_DICT.deepcopy()#instance of table

The last line must make a copy of class dictionary to store instance data in it, but it throws

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "./codon_usage.py", line 47, in __init__
    self.usage_table=CodonUsageTable.CODON_DICT.deepcopy()#instance of codon usage table
NameError: global name 'CODON_DICT' is not defined

So does self.CODON_DICT, CODON_DICT or codon_usage.CodonUsageTable.CODON_DICT, when called from __init__. Dictionary is defined:

>>>import codon_usage
>>> codon_usage.CodonUsageTable.CODON_DICT
{'GCT': 0, 'GGA': 0, 'TTA': 0, 'GAT': 0, 'TTC': 0, 'TTG': 0, 'AGT': 0, 'GCG': 0, 'AGG': 0, 'GCC': 0, 'CGA': 0, 'GCA': 0, 'GGC': 0, 'GAG': 0, 'GAA': 0, 'TTT': 0, 'GAC': 0, 'TAT': 0, 'CGC': 0, 'TGT': 0, 'TCA': 0, 'GGG': 0, 'TCC': 0, 'ACG': 0, 'TCG': 0, 'TAG': 0, 'TAC': 0, 'TAA': 0, 'ACA': 0, 'TGG': 0, 'TCT': 0, 'TGA': 0, 'TGC': 0, 'CTG': 0, 'CTC': 0, 'CTA': 0, 'ATG': 0, 'ATA': 0, 'ATC': 0, 'AGA': 0, 'CTT': 0, 'ATT': 0, 'GGT': 0, 'AGC': 0, 'ACT': 0, 'CGT': 0, 'GTT': 0, 'CCT': 0, 'AAG': 0, 'CGG': 0, 'AAC': 0, 'CAT': 0, 'AAA': 0, 'CCC': 0, 'GTC': 0, 'CCA': 0, 'GTA': 0, 'CCG': 0, 'GTG': 0, 'ACC': 0, 'CAA': 0, 'CAC': 0, 'AAT': 0, 'CAG': 0}        'GGT': 0, 'GGC': 0, 'GGA': 0, 'GGG': 0}

Answer 1

The symptoms imply that the story went like this:

1. you wrote the file and saved it;
2. you ran the Python shell;
3. you found that CODON_DICT can't be accessed just like that and fixed that;
4. you tried that call again within the same Python shell and got that error.

That happens because Python is still using the old version of the module, which is loaded during the import. Although it shows the line from the new file, since all it has in the memory is the bytecode with metadata and has to refer to the disk when error happens. If you want to pick your latest changes without restarting the shell, run:

>>> reload(codon_usage)

and try again.

(A sidenote: dict has no method deepcopy, that function comes from the module copy. dict.copy is enough here, though).