CODEWITHSUNDEEP
pythonsortingsubstring
Rick Tearle
Rick Tearle

Reputation: 65

Sorting a list of lists, using part of an element of the sublists

I have a list of lists. The first element in each sublist is a chromosome eg 'chr1', 'chr5', 'chr10', 'chrX' and 'chrY'. I want to sort the sublists by chromosome number and then by X and Y. I have tried the following.

List.sort(key=lambda x: Set_Chr_Nr_(x[0]))

I am using the following def, which takes the chromosome string, removes the 'chr', converts the remainder to an int if it is a number, and asssigns a number if it is an 'X' or 'Y'.

def Set_Chr_Nr_ (Chr):
    """ Sort by chromosome """
    if Chr: 
        New = Chr[3:]
        if New == 'X': New = 23
        elif New == 'Y': New = 24
        elif New == 'M': New = 25
        else: New = int(New)
    else:
        New = 0
    return New

But it does not return the desired sort order. Instead, I get a list that starts with sublists contiaing 'chr1' but puts sublists containing 'chr10' next, not 'chr2'. What am I doing wrong here?

Example data with column header:

Type    OriginChr   OriginBegin OriginEnd   DestChr DestBegin   DestEnd

inversion   chr10   13105010    13105143    chr10   13104876    13105378

inversion   chr14   87902496    87902539    chr14   87902497    87902540

Rick

Upvotes: 1

Views: 1118

Answers (1)

Qiang Jin
Qiang Jin

Reputation: 4467

You can try, 

a = ['chr1', 'chr10', 'chr5', 'chrX']
sorted(a, key=lambda x: Set_Chr_Nr_(x))
print a

If you want to use list.sort(), you can switch to,

a.sort(lambda x,y: x-y, key=lambda x: Set_Chr_Nr_(x))

For you original input, if the column is fixed, this will work,

a = [['inversion', 'chr14', 87902496, 87902539, 'chr14', 87902497, 87902540], ['inversion', 'chr10', 13105010, 13105143, 'chr10', 13104876, 13105378]]
sorted(a, key=lambda x: Set_Chr_Nr_(x[1]))
print a

Upvotes: 1

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