Python equivalent of bash sort lexicographical and numerical

Question

So I've been working on a Python script that combines some information into a "bed" format. Which means that I'm working with features on a genome, my first column is the scaffold name (string), the second the start position on that scaffold (integer) and the third column is the stop position (integer), the other columns contain other information which is not relevant to my question. My issue is that my output is unsorted.

Now I know I can sort my files using this bash command:

$sort -k1,1 -k2,2n -k3,3n infile > outfile

But in the interest efficacy I'd like to know if there's a way to do this in Python. So far I've only seen list based sorts that deal with one either lexicographical or numerical sort. Not a combination of the two. So, do you guys have any ideas?

Snippet of my data (I want to sort by column 1, 2 and 3 (in that order)):

Scf_3R  8599253 8621866 FBgn0000014 FBgn0191744 -0.097558026153
Scf_3R  8497493 8503049 FBgn0000015 FBgn0025043 0.437973284047
Scf_3L  16209309    16236428    FBgn0000017 FBgn0184183 -1.19105585707
Scf_2L  10630469    10632308    FBgn0000018 FBgn0193617 0.073153454539
Scf_3R  12087670    12124207    FBgn0000024 FBgn0022516 -0.023946795475
Scf_X   14395665    14422243    FBgn0000028 FBgn0187465 0.00300558969397
Scf_3R  25163062    25165316    FBgn0000032 FBgn0189058 0.530118698187
Scf_3R  19757441    19808894    FBgn0000036 FBgn0189822 -0.282508464261

Answer 1

Load data, sort them with sorted, write to a new file.

# Load data 
lists = list()
with open(filename, 'r') as f:
    for line in f:
        lists.append(line.rstrip().split())

# Sort data
results = sorted(lists, key=lambda x:(x[0], int(x[1]), int(x[2])))

# Write to a file
import csv
with open(filename, 'w') as f:
    writer = csv.writer(f, delimiter='\t')
    writer.writerows(results)