Rearrange strings in list alphabetically and by case

Question

I have a list in a for loop and it uses itertools.product() to find different combinations of letters. I want to use collections.Counter() to count the number of occurrences of an item, however, right now it prints all the different combinations of "A"'s and "G"'s:

['a', 'A', 'G', 'G']
['a', 'A', 'G', 'g']
['a', 'A', 'G', 'G']
['a', 'A', 'G', 'g']
['a', 'A', 'G', 'g']
#...
['a', 'G', 'A', 'G']
['a', 'G', 'a', 'g']
['a', 'G', 'A', 'G']
['a', 'G', 'a', 'G']
['a', 'G', 'a', 'G']
#...
['a', 'G', 'a', 'G']
['a', 'G', 'A', 'G']
['a', 'G', 'a', 'g']
['a', 'G', 'A', 'G']
['a', 'G', 'a', 'G']
#...
['a', 'G', 'A', 'G']
['a', 'G', 'a', 'G']
['a', 'G', 'a', 'G']
# etc.

Now, this isn't all of them, but as you can see, there are some occurrences that are the same although ordered differently, for example:

['a', 'G', 'A', 'G']
['a', 'A', 'G', 'G']

I would much prefer the latter ordering, so I want to find a way to print all of the combinations with capital letters before lower case, and because 'a' is before 'g', also alphabetically. The final product should look like ['AaGG', 'aaGg', etc]. What function or functions should I use?

This is the code that generates the data. The section marked "Counting" is what I'm having trouble with.

import itertools
from collections import Counter
parent1 = 'aaGG'
parent2 = 'AaGg'
f1 = []
f1_ = []
genotypes = []
b = []
genetics = []
g = []
idx = []

parent1 = list(itertools.combinations(parent1, 2))    
del parent1[0]
del parent1[4] 

parent2 = list(itertools.combinations(parent2, 2))    
del parent2[0]
del parent2[4]


for x in parent1:
    f1.append(''.join(x))

for x in parent2:
    f1_.append(''.join(x))

y = list(itertools.product(f1, f1_))  

for x in y:
    genotypes.append(''.join(x))
    break
genotypes = [
        thingies[0][0] + thingies[1][0] + thingies[0][1] + thingies[1][1]
        for thingies in zip(parent1, parent2)
] * 4
print 'F1', Counter(genotypes)

# Counting
for genotype in genotypes:
    alleles = list(itertools.combinations(genotype,2))
    del alleles[1]
    del alleles[3]
    for x in alleles:
        g.append(''.join(x))

for idx in g:
    if idx.lower().count("a") == idx.lower().count("g") == 1:
        break                

f2 = list(itertools.product(g, g)) 

for x in f2:
    genetics.append(''.join(x)) 

for genes in genetics:
    if genes.lower().count("a") == genes.lower().count("g") == 2:
        genes = ''.join(genes)
    print Counter(genes)

Answer 1

I think you're looking for a customized way to define precedence; the lists are currently being ordered by ASCII numbering, which defines uppercase letters as always preceding lowercase letters. I would define customized precedence using a dictionary:

>>> test_list = ['a', 'A', 'g', 'G']
>>> precedence_dict = {'A':0, 'a':1, 'G':2,'g':3}
>>> test_list.sort(key=lambda x: precedence_dict[x])
>>> test_list
['A', 'a', 'G', 'g']

Edit: Your last few lines:

for genes in genetics:
    if genes.lower().count("a") == genes.lower().count("g") == 2:
        genes = ''.join(genes)
    print Counter(genes)

were not doing what you wanted them to.

Replace those lines with:

precedence_dict = {'A':0, 'a':1, 'G':2,'g':3}

for i in xrange(len(genetics)):
    genetics[i] = list(genetics[i])
    genetics[i].sort(key=lambda x: precedence_dict[x])
    genetics[i] = ''.join(genetics[i])
from sets import Set

genetics = list(Set(genetics))
genetics.sort()

print genetics

and I think you have the correct solution. When iterating over elements in a for loop, Python makes a copy of the item. So the string 'genes' was actually not being modified in the original list.

Answer 2

I know you didn't ask for a code review, but you might be better off just generating the strings in the order you want in the first place instead of trying to filter them afterwards. Something like this might work.

def cross(parent1, parent2):

    out = []
    alleles = len(parent1)/2

    # iterate parent 1 possible genotypes
    for i in range(2):

        # iterate loci 
        for k in range(alleles):
            child = []

            # iterate parent 2 possible genotypes
            for j in range(2):
                p1 = parent1[j * 2 + i]
                p2 = parent2[j * 2 + k]
                c = [p1, p2]

                # get each genotype pair into capitalization order
                c.sort()
                c.reverse()
                child += c

            out.append("".join(child))
    return out


if __name__ == "__main__":

    parent1 = 'aaGG'
    parent2 = 'AaGg'

    # F1
    f1 = cross(parent1, parent2)
    print f1

    # F2
    f2 = []
    for p1 in f1:
        for p2 in f1:
            f2 += cross(p1, p2)
    print f2

Here's one way to get all combinations from a single parent. Start with the empty string and add the possibilities one by one.

def get_all_combos(allele_pair, gametes):
# Take a list of of genotypes. Return an updated list with each possibility from an allele pair

    updated_gametes = []
    for z in gametes:
       updated_gametes.append(z + allele_pair[0])
       updated_gametes.append(z + allele_pair[1])
    return updated_gametes

if __name__ == "__main__":

    parent1 = 'aaGG'
    parent2 = 'AaGg'

    alleles = len(parent2)/2
    gametes = [""]
    for a in range(alleles):
        allele_pair = parent2[a*2:a*2+2]
        gametes = get_all_combos(allele_pair, gametes)
    print gametes

Maybe you can figure out how to combine these two solutions to get what you want.

Answer 3

you can try using the sort function. Example of what I mean:

parent1 = "absdksakjcvjvugoh"
parent1sorted = list(parent1)
parent1sorted.sort()
print (parent1sorted)

The result you get is this : ['a', 'a', 'b', 'c', 'd', 'g', 'h', 'j', 'j', 'k', 'k', 'o', 's', 's', 'u', 'v', 'v']

Does this help you?

tldr: Convert string into list, Sort list