linux rearange field and sort by column

Question

I have (tab-separated) input files:

id1 id2 ....
id1 id3 ....
id3 id4 ....
id2 id1 ....
id3 id4 ....
.....

I need to

1. rearrange col1 and col2 by numerical sort. For now I do this in a python script.
2. sort by col1 then col2. For now I am doing this by taking the output of the python script and using GNU sort.

My question is the following: is there a way to merge step 1 and step 2 (using GNU sort or any other GNU/Linux command-line tools)?

Is there an efficient alternative GNU/Linux command for step 1?

result:
id1 id2 ....
id1 id2 ....
id1 id3 .... 
id3 id4 ....
id3 id4 ....
.....

My code actually works, I am looking to improve its speed.

Here's the Python program:

import argparse
import subprocess
import os
parser = argparse.ArgumentParser(description='')
parser.add_argument('-blast', help='input', required=True)
parser.add_argument('-out', help='output', required=True)
args = parser.parse_args()
def get_tmp():
# return a name for temporary file.
 dir = os.listdir(".")
 cpt = 0
 name = "tmp_{}".format(cpt)
 while name in dir:
 cpt += 1
 name = "tmp_{}".format(cpt)
 return name
# get a temporary name
tmp_name = get_tmp()
# open inputfile in reading and output in writing
with open(args.blast) as input_blast, open(tmp_name, 'w') as tmp_file:
 for line in input_blast:
 spt = line.strip().split()
 tmp_file.write('\t'.join(sorted(spt[0:2]) + spt[2:]) + '\n')
# sort by field one and two
child = subprocess.Popen("sort -k1 -k2 {} > temps_sort && mv temps_sort {}".format(os.path.abspath(tmp_name), args.out),shell=True)
child.wait()

• Maarten Fabré: PS no need to create your own temp-file handling. python standard library has a tempfile module

Answer 1

There is no reason to use an external file and command. Python can sort strings just fine, unless the file is too big

something like this should work

def rearrange_ids(file):
 pattern = re.compile(r'id(\d+)')
 for line in file:
 spt = line.strip().split()
 if spt:
 ids = sorted(int(pattern.findall(id_string)[0]) for id_string in spt[0:2])
 yield ids, '\t'.join(['id%i' % i for i in ids] + spt[2:]) + '\n'
with open(input_file, 'r') as file, open(output_filename, 'w') as output_file:
 output_lines = sorted(rearrange_ids(file), key=lambda x: x[0])
 output_file.writelines(line for ids, line in output_lines)

id1 id2 ....
id1 id2 ....
id1 id3 ....
id3 id4 ....
id3 id4 ....

edit

I changed my original algorithm because id did not keep the original order when comparing, and sorted 10 before 2