An efficient way to transpose a file in Bash
A Python solution:
python -c "import sys; print('\n'.join(' '.join(c) for c in zip(*(l.split() for l in sys.stdin.readlines() if l.strip()))))" < input > output
The above is based on the following:
import sys
for c in zip(*(l.split() for l in sys.stdin.readlines() if l.strip())):
print(' '.join(c))
This code does assume that every line has the same number of columns (no padding is performed).
awk '
{
for (i=1; i<=NF; i++) {
a[NR,i] = $i
}
}
NF>p { p = NF }
END {
for(j=1; j<=p; j++) {
str=a[1,j]
for(i=2; i<=NR; i++){
str=str" "a[i,j];
}
print str
}
}' file
output
$ more file
0 1 2
3 4 5
6 7 8
9 10 11
$ ./shell.sh
0 3 6 9
1 4 7 10
2 5 8 11
Performance against Perl solution by Jonathan on a 10000 lines file
$ head -5 file
1 0 1 2
2 3 4 5
3 6 7 8
4 9 10 11
1 0 1 2
$ wc -l < file
10000
$ time perl test.pl file >/dev/null
real 0m0.480s
user 0m0.442s
sys 0m0.026s
$ time awk -f test.awk file >/dev/null
real 0m0.382s
user 0m0.367s
sys 0m0.011s
$ time perl test.pl file >/dev/null
real 0m0.481s
user 0m0.431s
sys 0m0.022s
$ time awk -f test.awk file >/dev/null
real 0m0.390s
user 0m0.370s
sys 0m0.010s
EDIT by Ed Morton (@ghostdog74 feel free to delete if you disapprove).
Maybe this version with some more explicit variable names will help answer some of the questions below and generally clarify what the script is doing. It also uses tabs as the separator which the OP had originally asked for so it'd handle empty fields and it coincidentally pretties-up the output a bit for this particular case.
$ cat tst.awk
BEGIN { FS=OFS="\t" }
{
for (rowNr=1;rowNr<=NF;rowNr++) {
cell[rowNr,NR] = $rowNr
}
maxRows = (NF > maxRows ? NF : maxRows)
maxCols = NR
}
END {
for (rowNr=1;rowNr<=maxRows;rowNr++) {
for (colNr=1;colNr<=maxCols;colNr++) {
printf "%s%s", cell[rowNr,colNr], (colNr < maxCols ? OFS : ORS)
}
}
}
$ awk -f tst.awk file
X row1 row2 row3 row4
column1 0 3 6 9
column2 1 4 7 10
column3 2 5 8 11
The above solutions will work in any awk (except old, broken awk of course - there YMMV).
The above solutions do read the whole file into memory though - if the input files are too large for that then you can do this:
$ cat tst.awk
BEGIN { FS=OFS="\t" }
{ printf "%s%s", (FNR>1 ? OFS : ""), $ARGIND }
ENDFILE {
print ""
if (ARGIND < NF) {
ARGV[ARGC] = FILENAME
ARGC++
}
}
$ awk -f tst.awk file
X row1 row2 row3 row4
column1 0 3 6 9
column2 1 4 7 10
column3 2 5 8 11
which uses almost no memory but reads the input file once per number of fields on a line so it will be much slower than the version that reads the whole file into memory. It also assumes the number of fields is the same on each line and it uses GNU awk for ENDFILE and ARGIND but any awk can do the same with tests on FNR==1 and END.
awk
Gawk version which uses arrays of arrays:
tp(){ awk '{for(i=1;i<=NF;i++)a[i][NR]=$i}END{for(i in a)for(j in a[i])printf"%s"(j==NR?RS:FS),a[i][j]}' "${1+FS=$1}";}
Plain awk version which uses multidimensional arrays (this was about twice as slow in my benchmark):
tp(){ awk '{for(i=1;i<=NF;i++)a[i,NR]=$i}END{for(i=1;i<=NF;i++)for(j=1;j<=NR;j++)printf"%s"(j==NR?RS:FS),a[i,j]}' "${1+FS=$1}";}
macOS comes with a version of Brian Kerningham's nawk from 2007 which doesn't support arrays of arrays.
To use space as a separator without collapsing sequences of multiple spaces, use FS='[ ]'.
rs
rs is a BSD utility which also comes with macOS, but it should be available from package managers on other platforms. It is named after the reshape function in APL.
Use sequences of spaces and tabs as column separator:
rs -T
Use tab as column separator:
rs -c -C -T
Use comma as column separator:
rs -c, -C, -T
-c changes the input column separator and -C changes the output column separator. A lone -c or -C sets the separator to tab. -T transposes rows and columns.
Do not use -t instead of -T, because it automatically selects the number of output columns so that the output lines fill the width of the display (which is 80 characters by default but which can be changed with -w).
When an output column separator is specified using -C, an extra column separator character is added to the end of each row, but you can remove it with sed:
$ seq 4|paste -d, - -|rs -c, -C, -T
1,3,
2,4,
$ seq 4|paste -d, - -|rs -c, -C, -T|sed s/.\$//
1,3
2,4
rs -T determines the number of columns based on the number of columns on the first row, so it produces the wrong result when the first line ends with one or more empty columns:
$ rs -c, -C, -T<<<$'1,\n3,4'
1,3,4,
R
The t function transposes a matrix or dataframe:
Rscript -e 'write.table(t(read.table("stdin",sep=",",quote="",comment.char="")),sep=",",quote=F,col.names=F,row.names=F)'
If you replace Rscript -e with R -e, then it echoes the code that is being run to STDOUT, and it also results in the error ignoring SIGPIPE signal if the R command is followed by a command like head -n1 which exits before it has read the whole STDIN.
quote="" can be removed if the input doesn't contain double quotes or single quotes, and comment.char="" can be removed if the input doesn't contain lines that start with a hash character.
For a big input file, fread and fwrite from data.table are faster than read.table and write.table:
$ seq 1e6|awk 'ORS=NR%1e3?FS:RS'>a
$ time Rscript --no-init-file -e 'write.table(t(read.table("a")),quote=F,col.names=F,row.names=F)'>/dev/null
real 0m1.061s
user 0m0.983s
sys 0m0.074s
$ time Rscript --no-init-file -e 'write.table(t(data.table::fread("a")),quote=F,col.names=F,row.names=F)'>/dev/null
real 0m0.599s
user 0m0.535s
sys 0m0.048s
$ time Rscript --no-init-file -e 'data.table::fwrite(t(data.table::fread("a")),sep=" ",col.names=F)'>t/b
x being coerced from class: matrix to data.table
real 0m0.375s
user 0m0.296s
sys 0m0.073s
jq
tp(){ jq -R .|jq --arg x "${1-$'\t'}" -sr 'map(./$x)|transpose|map(join($x))[]';}
jq -R . prints each input line as a JSON string literal, -s (--slurp) creates an array for the input lines after parsing each line as JSON, and -r (--raw-output) outputs the contents of strings instead of JSON string literals. The / operator is overloaded to split strings.
Ruby
ruby -e'STDIN.map{|x|x.chomp.split(",",-1)}.transpose.each{|x|puts x*","}'
The -1 argument to split disables discarding empty fields at the end:
$ ruby -e'p"a,,".split(",")'
["a"]
$ ruby -e'p"a,,".split(",",-1)'
["a", "", ""]
Function form:
$ tp(){ ruby -e's=ARGV[0];STDIN.map{|x|x.chomp.split(s==" "?/ /:s,-1)}.transpose.each{|x|puts x*s}' -- "${1-$'\t'}";}
$ seq 4|paste -d, - -|tp ,
1,3
2,4
The function above uses s==" "?/ /:s because when the argument to the split function is a single space, it enables awk-like special behavior where strings are split based on contiguous runs of spaces and tabs:
$ ruby -e'p" a \tb ".split(" ",-1)'
["a", "b", ""]
$ ruby -e'p" a \tb ".split(/ /,-1)'
["", "a", "", "\tb", ""]