Sorting a list of chromsomes in the correct order-CodePudding

A seemingly simple problem, but one that's proving a bit vexing. I have a list of chromosomes (there are 23 chromosome - chromosomes 1 to 21, then chromosome X and chromosome Y) like so:

['chr11','chr14','chr16','chr13','chr4','chr13','chr2','chr1','chr2','chr3','chr14','chrX',]

I would like to sort this in the following order :

['chr1', 'chr2','chr2','chr3','chr4','chr11','chr13','chr13', 'chr14','chr14','chr16','chrX']

However, due to the lexicographical nature of python's sort it will sort chr1, chr10, chr11, chr12...chr2, etc. as I have chromosome X, sorting by their integer values also doesn't seem like an option. would I potentially have to specify a unique key by which to sort the list? Or is there some sort of obvious solution I'm missing

As always, any help is much appreciated!

CodePudding user response：

You can use natsorted, what you want is natural sorting after all ;)

l = ['chr11','chr14','chr16','chr13','chr4','chr13','chr2',
     'chr1','chr2','chr3','chr14','chrX','chrY']

from natsort import natsorted

out = natsorted(l)

output:

['chr1', 'chr2', 'chr2', 'chr3', 'chr4', 'chr11', 'chr13',
 'chr13', 'chr14', 'chr14', 'chr16', 'chrX', 'chrY']

CodePudding user response：

You can create a custom key:

key={s:i for i,s in 
    enumerate([f'chr{x}' for x in list(range(1,22)) ['X','Y']],1)}

>>> key
{'chr1': 1, 'chr2': 2, 'chr3': 3, 'chr4': 4, 'chr5': 5, 'chr6': 6, 'chr7': 7, 'chr8': 8, 'chr9': 9, 'chr10': 10, 'chr11': 11, 'chr12': 12, 'chr13': 13, 'chr14': 14, 'chr15': 15, 'chr16': 16, 'chr17': 17, 'chr18': 18, 'chr19': 19, 'chr20': 20, 'chr21': 21, 'chrX': 22, 'chrY': 23}

Then use that key as a lookup in sorted:

li = ['chr11','chr14','chr16','chr13','chr4','chr13','chr2',
     'chr1','chr2','chr3','chr14','chrX','chrY']

>>> sorted(li, key=lambda s: key[s])
['chr1', 'chr2', 'chr2', 'chr3', 'chr4', 'chr11', 'chr13', 'chr13', 'chr14', 'chr14', 'chr16', 'chrX', 'chrY']

CodePudding user response：

natsort as already mentioned by @mozway is the fastest way.

Here the solution without using external libraries.

sorted(l, key=lambda x: int(val) if (val:=x[3:]).isnumeric() else ord(val))

It gives the same output.

CodePudding user response：

You could try to replace X and Y for 22 and 23 respectly inside a lambda function that then replace the char values for nothing and then use only the int part of the string to sort the list

l = ['chr1', 'chr2','chr2','chr3','chr4','chr11','chr13','chr13', 'chr14','chr14','chr16','chrX']

sorted( l, key= lambda x: int(x.replace('X','22').replace('Y','23').replace('chr','')))

# OUTPUT
['chr1', 'chr2', 'chr2', 'chr3', 'chr4', 'chr11', 'chr13', 'chr13', 'chr14', 'chr14', 'chr16','chrX']

CodePudding user response：

you can use this human sorting like this :

    import re

def atoi(text):
    return int(text) if text.isdigit() else text

def natural_keys(text):
    '''
    alist.sort(key=natural_keys) sorts in human order
    http://nedbatchelder.com/blog/200712/human_sorting.html
    (See Toothy's implementation in the comments)
    '''
    return [ atoi(c) for c in re.split(r'(\d )', text) ]

alist=['chr11','chr14','chr16','chr13','chr4','chr13','chr2','chr1','chr2','chr3','chr14','chrX',]

alist.sort(key=natural_keys)
print(alist)

output:
['chr1', 'chr2', 'chr2', 'chr3', 'chr4', 'chr11', 'chr13', 'chr13', 'chr14', 'chr14', 'chr16', 'chrX', 'chrY']

or you can using natstor(github) natstor(lib) like this:

   import natsort 
   list=['chr11','chr14','chr16','chr13','chr4','chr13','chr2',
     'chr1','chr2','chr3','chr14','chrX','chrY']
    result=natsort.natsorted(list)
    print(result)

output:
['chr1', 'chr2', 'chr2', 'chr3', 'chr4', 'chr11', 'chr13', 'chr13', 'chr14', 'chr14', 'chr16', 'chrX', 'chrY']