Swap two columns - awk, sed, python, perl

Question

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

Answer 1

You can do this by swapping values of the first two fields:

awk ' { t = $1; $1 = $2; $2 = t; print; } ' input_file

Answer 2

I tried the answer of perreal with cygwin on a windows system with a tab separated file. It didn't work, because the standard separator is space.

If you encounter the same problem, try this instead:

awk -F $'\t' ' { t = $1; $1 = $2; $2 = t; print; } ' OFS=$'\t' input_file

Incoming separator is defined by -F $'\t' and the seperator for output by OFS=$'\t'.

awk -F $'\t' ' { t = $1; $1 = $2; $2 = t; print; } ' OFS=$'\t' input_file > output_file

Answer 3

Try this more relevant to your question :

awk '{printf("%s\t%s\n", $2, $1)}' inputfile

Answer 4

This might work for you (GNU sed):

sed -i 's/^\([^\t]*\t\)\([^\t]*\t\)/\2\1/' file

Answer 5

Have you tried using the cut command? E.g.

cat myhugefile | cut -c10-20,c1-9,c21- > myrearrangedhugefile

Answer 6

This is also easy in perl:

perl -pe 's/^(\S+)\t(\S+)/$2\t$1/;' file > outputfile

Answer 7

You could do this in Perl:

perl -F\\t -nlae 'print join("\t", @F[1,0,2..$#F])' inputfile

The -F specifies the delimiter. In most shells you need to precede a backslash with another to escape it. On some platforms -F automatically implies -n and -a so they can be dropped.

For your problem you wouldn't need to use -l because the last columns appears last in the output. But if in a different situation, if the last column needs to appear between other columns, the newline character must be removed. The -l switch takes care of this.

The "\t" in join can be changed to anything else to produce a different delimiter in the output.

2..$#F specifies a range from 2 until the last column. As you might have guessed, inside the square brackets, you can put any single column or range of columns in the desired order.

Answer 8

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

Answer 9

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, ...

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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.