Swap two columns - awk, sed, python, perl

user_1517596 0
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I've got data in a large file (280 columns wide, 7 million lines long!) and I need to swap the first two columns. I think I could do this with some kind of awk for loop, to print $2, $1, then a range to the end of the file - but I don't know how to do the range part, and I can't print $2, $1, $3...$280! Most of the column swap answers I've seen here are specific to small files with a manageable number of columns, so I need something that doesn't depend on specifying every column number.

The file is tab delimited:

Affy-id chr 0 pos NA06984 NA06985 NA06986 NA06989
sed awk
9 Answers

No need to call anything else but your shell:

bash> while read col1 col2 rest; do 
        echo $col2 $col1 $rest
      done <input_file

Test:

bash> echo "first second a c d e f g" | 
      while read col1 col2 rest; do 
        echo $col2 $col1 $rest
      done
second first a b c d e f g
user_126245950

Maybe even with "inlined" Python - as in a Python script within a shell script - but only if you want to do some more scripting with Bash beforehand or afterwards... Otherwise it is unnecessarily complex.

Content of script file process.sh:

#!/bin/bash

# inline Python script
read -r -d '' PYSCR << EOSCR
from __future__ import print_function
import codecs
import sys

encoding = "utf-8"
fn_in = sys.argv[1]
fn_out = sys.argv[2]

# print("Input:", fn_in)
# print("Output:", fn_out)

with codecs.open(fn_in, "r", encoding) as fp_in, \
        codecs.open(fn_out, "w", encoding) as fp_out:
    for line in fp_in:
        # split into two columns and rest
        col1, col2, rest = line.split("\t", 2)
        # swap columns in output
        fp_out.write("{}\t{}\t{}".format(col2, col1, rest))
EOSCR

# ---------------------
# do setup work?
# e. g. list files for processing

# call python script with params
python3 -c "$PYSCR" "$inputfile" "$outputfile"

# do some more processing
# e. g. rename outputfile to inputfile, ...

If you only need to swap the columns for a single file, then you can also just create a single Python script and statically define the filenames. Or just use an answer above.

user_93601610
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