Making a dictionary from a list of lists

Question

I have been unable to figure this out, I think the problem might be in the way I am making the list of lists. Can anyone help out? Thanks!

My desired outcome is

codondict = {'A': ['GCT','GCC','GCA','GCG'], 'C': ['TGT','TGC'], &c

but what i get is:

{'A': 'A', 'C': 'C', &c.

Here's my terminal:

A=['GCT','GCC','GCA','GCG']

C=['TGT','TGC']

D=['GAT','GAC']

E=['GAA','GAG']

F=['TTT','TTC']

G=['GGT','GGC','GGA','GGG']

H=['CAT','CAC']

I=['ATT','ATC','ATA']

K=['AAA','AAG']

L=['TTA','TTG','CTT','CTC','CTA','CTG']

M=['ATG']

N=['AAT','AAC']

P=['CCT','CCC','CCA','CCG']

Q=['CAA','CAG']

R=['CGT','CGC','CGA','CGG','AGA','AGG']

S=['TCT','TCC','TCA','TCG','AGT','AGC']

T=['ACT','ACC','ACA','ACG']

V=['GTT','GTC','GTA','GTG']

W=['TGG']

Y=['TAT','TAC']

aminoacids=['A','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','Y']

from collections import defaultdict

codondict=defaultdict(list)

for i in aminoacids:

... for j in i:(ALSO TRIED for j in list(i))

... ... codondict[i]=j ...

codondict

defaultdict(, {'A': 'A', 'C': 'C', 'E': 'E', 'D': 'D', 'G': 'G', 'F': 'F', 'I': 'I', 'H': 'H', 'K': 'K', 'M': 'M', 'L': 'L', 'N': 'N', 'Q': 'Q', 'P': 'P', 'S': 'S', 'R': 'R', 'T': 'T', 'W': 'W', 'V': 'V', 'Y': 'Y'})

Answer 1

You can try this:

condondict= dict(A=['GCT','GCC','GCA','GCG'],
C=['TGT','TGC'],
D=['GAT','GAC'],
E=['GAA','GAG'],
F=['TTT','TTC'],
G=['GGT','GGC','GGA','GGG'],
H=['CAT','CAC'],
I=['ATT','ATC','ATA'],
K=['AAA','AAG'],
L=['TTA','TTG','CTT','CTC','CTA','CTG'],
M=['ATG'],
N=['AAT','AAC'],
P=['CCT','CCC','CCA','CCG'],
Q=['CAA','CAG'],
R=['CGT','CGC','CGA','CGG','AGA','AGG'],
S=['TCT','TCC','TCA','TCG','AGT','AGC'],
T=['ACT','ACC','ACA','ACG'],
V=['GTT','GTC','GTA','GTG'],
W=['TGG'],
Y=['TAT','TAC'])

The reason to use defaultdict() is to allow access/creation of dictionary values without causing a KeyError, or by-pass using the form:

if key not in mydict.keys():
    mydict[key] = []
mydict[key].append(something)

If your not creating new keys dynamically, you don't really need to use defaultdict() .

Also if your keys already represent the aminoacids , you and just iterate over the keys themselves.

for aminoacid, sequence in condondict.iteritems():
    # do stuff with with data...

Answer 2

Another way to do what you need is using the locals() function, which returns a dictionary containing the whole set of variables of the local scope, with the variable names as the keys and its contents as values.

for i in aminoacids:
    codondict[i] = locals()[i]

So, you could get the A list, for example, using: locals()['A'] .

Answer 3

That's kind of verbose, and is confusing the name of a variable 'A' with its value A . Keeping to what you've got:

aminoacids = { 'A': A, 'C': C, 'D': D ... }

should get you the dictionary you ask for:

{ 'A' : ['GCT', 'GCC', 'GCA', 'GCG'], 'C' : ['TGT', 'TGC'], ... }

where the order of keys 'A' and 'C' may not be what you get back because dictionaries are not ordered.

Answer 4

You can use globals() built-in too, and dict comprehension:

codondict = {k:globals()[k] for k in aminoacids}

it's better to rely on locals() instead of globals(), like stummjr's solution, but you can't do so with dict comprehension directly

codondict = dict([(k,locals()[k]) for k in aminoacids])

However you can do this:

loc = locals()
codondict = {k:loc[k] for k in aminoacids}

If you change dinamically your aminoacids list or the aminoacids assignments, it's better to use something lazier, like:

codondict = lambda: {k:globals()[k] for k in aminoacids}

with this last you can always use the updated dictionary, but it's now a callable, so use codondict()[x] instead of codondict[x] to get an actual dict. This way you can store the entire dict like hist = codondict() in case you need to compare different historical versions of codondict. That's small enough to be useful in interactive modes, but not recommended in bigger codes, though.