I have a huge tab-separated file formatted like this
X column1 column2 column3
row1 0 1 2
row2 3 4 5
row3 6 7 8
row4 9 10 11
I would like to transpose it in an efficient way using only bash commands (I could write a ten or so lines Perl script to do that, but it should be slower to execute than the native bash functions). So the output should look like
X row1 row2 row3 row4
column1 0 3 6 9
column2 1 4 7 10
column3 2 5 8 11
I thought of a solution like this
cols=`head -n 1 input | wc -w`
for (( i=1; i <= $cols; i++))
do cut -f $i input | tr $'\n' $'\t' | sed -e "s/\t$/\n/g" >> output
done
But it's slow and doesn't seem the most efficient solution. I've seen a solution for vi in this post, but it's still over-slow. Any thoughts/suggestions/brilliant ideas? :-)
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", ""]
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).
Have a look at GNU datamash which can be used like datamash transpose.
A future version will also support cross tabulation (pivot tables)
Here is how you would do it with space separated columns:
datamash transpose -t ' ' < file > transposed_file
the transpose project on sourceforge is a coreutil-like C program for exactly that.
gcc transpose.c -o transpose
./transpose -t input > output #works with stdin, too.
Pure BASH, no additional process. A nice exercise:
declare -a array=( ) # we build a 1-D-array
read -a line < "$1" # read the headline
COLS=${#line[#]} # save number of columns
index=0
while read -a line ; do
for (( COUNTER=0; COUNTER<${#line[#]}; COUNTER++ )); do
array[$index]=${line[$COUNTER]}
((index++))
done
done < "$1"
for (( ROW = 0; ROW < COLS; ROW++ )); do
for (( COUNTER = ROW; COUNTER < ${#array[#]}; COUNTER += COLS )); do
printf "%s\t" ${array[$COUNTER]}
done
printf "\n"
done
GNU datamash is perfectly suited for this problem with only one line of code and potentially arbitrarily large filesize!
datamash -W transpose infile > outfile
There is a purpose built utility for this,
GNU datamash utility
apt install datamash
datamash transpose < yourfile
Taken from this site, https://www.gnu.org/software/datamash/ and http://www.thelinuxrain.com/articles/transposing-rows-and-columns-3-methods
Here is a moderately solid Perl script to do the job. There are many structural analogies with #ghostdog74's awk solution.
#!/bin/perl -w
#
# SO 1729824
use strict;
my(%data); # main storage
my($maxcol) = 0;
my($rownum) = 0;
while (<>)
{
my(#row) = split /\s+/;
my($colnum) = 0;
foreach my $val (#row)
{
$data{$rownum}{$colnum++} = $val;
}
$rownum++;
$maxcol = $colnum if $colnum > $maxcol;
}
my $maxrow = $rownum;
for (my $col = 0; $col < $maxcol; $col++)
{
for (my $row = 0; $row < $maxrow; $row++)
{
printf "%s%s", ($row == 0) ? "" : "\t",
defined $data{$row}{$col} ? $data{$row}{$col} : "";
}
print "\n";
}
With the sample data size, the performance difference between perl and awk was negligible (1 millisecond out of 7 total). With a larger data set (100x100 matrix, entries 6-8 characters each), perl slightly outperformed awk - 0.026s vs 0.042s. Neither is likely to be a problem.
Representative timings for Perl 5.10.1 (32-bit) vs awk (version 20040207 when given '-V') vs gawk 3.1.7 (32-bit) on MacOS X 10.5.8 on a file containing 10,000 lines with 5 columns per line:
Osiris JL: time gawk -f tr.awk xxx > /dev/null
real 0m0.367s
user 0m0.279s
sys 0m0.085s
Osiris JL: time perl -f transpose.pl xxx > /dev/null
real 0m0.138s
user 0m0.128s
sys 0m0.008s
Osiris JL: time awk -f tr.awk xxx > /dev/null
real 0m1.891s
user 0m0.924s
sys 0m0.961s
Osiris-2 JL:
Note that gawk is vastly faster than awk on this machine, but still slower than perl. Clearly, your mileage will vary.
Assuming all your rows have the same number of fields, this awk program solves the problem:
{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}
In words, as you loop over the rows, for every field f grow a ':'-separated string col[f] containing the elements of that field. After you are done with all the rows, print each one of those strings in a separate line. You can then substitute ':' for the separator you want (say, a space) by piping the output through tr ':' ' '.
Example:
$ echo "1 2 3\n4 5 6"
1 2 3
4 5 6
$ echo "1 2 3\n4 5 6" | awk '{for (f=1;f<=NF;f++) col[f] = col[f]":"$f} END {for (f=1;f<=NF;f++) print col[f]}' | tr ':' ' '
1 4
2 5
3 6
If you have sc installed, you can do:
psc -r < inputfile | sc -W% - > outputfile
I normally use this little awk snippet for this requirement:
awk '{for (i=1; i<=NF; i++) a[i,NR]=$i
max=(max<NF?NF:max)}
END {for (i=1; i<=max; i++)
{for (j=1; j<=NR; j++)
printf "%s%s", a[i,j], (j==NR?RS:FS)
}
}' file
This just loads all the data into a bidimensional array a[line,column] and then prints it back as a[column,line], so that it transposes the given input.
This needs to keep track of the maximum amount of columns the initial file has, so that it is used as the number of rows to print back.
A hackish perl solution can be like this. It's nice because it doesn't load all the file in memory, prints intermediate temp files, and then uses the all-wonderful paste
#!/usr/bin/perl
use warnings;
use strict;
my $counter;
open INPUT, "<$ARGV[0]" or die ("Unable to open input file!");
while (my $line = <INPUT>) {
chomp $line;
my #array = split ("\t",$line);
open OUTPUT, ">temp$." or die ("unable to open output file!");
print OUTPUT join ("\n",#array);
close OUTPUT;
$counter=$.;
}
close INPUT;
# paste files together
my $execute = "paste ";
foreach (1..$counter) {
$execute.="temp$counter ";
}
$execute.="> $ARGV[1]";
system $execute;
The only improvement I can see to your own example is using awk which will reduce the number of processes that are run and the amount of data that is piped between them:
/bin/rm output 2> /dev/null
cols=`head -n 1 input | wc -w`
for (( i=1; i <= $cols; i++))
do
awk '{printf ("%s%s", tab, $'$i'); tab="\t"} END {print ""}' input
done >> output
Some *nix standard util one-liners, no temp files needed. NB: the OP wanted an efficient fix, (i.e. faster), and the top answers are usually faster than this answer. These one-liners are for those who like *nix software tools, for whatever reasons. In rare cases, (e.g. scarce IO & memory), these snippets can actually be faster than some of the top answers.
Call the input file foo.
If we know foo has four columns:
for f in 1 2 3 4 ; do cut -d ' ' -f $f foo | xargs echo ; done
If we don't know how many columns foo has:
n=$(head -n 1 foo | wc -w)
for f in $(seq 1 $n) ; do cut -d ' ' -f $f foo | xargs echo ; done
xargs has a size limit and therefore would make incomplete work with a long file. What size limit is system dependent, e.g.:
{ timeout '.01' xargs --show-limits ; } 2>&1 | grep Max
Maximum length of command we could actually use: 2088944
tr & echo:
for f in 1 2 3 4; do cut -d ' ' -f $f foo | tr '\n\ ' ' ; echo; done
...or if the # of columns are unknown:
n=$(head -n 1 foo | wc -w)
for f in $(seq 1 $n); do
cut -d ' ' -f $f foo | tr '\n' ' ' ; echo
done
Using set, which like xargs, has similar command line size based limitations:
for f in 1 2 3 4 ; do set - $(cut -d ' ' -f $f foo) ; echo $# ; done
I used fgm's solution (thanks fgm!), but needed to eliminate the tab characters at the end of each row, so modified the script thus:
#!/bin/bash
declare -a array=( ) # we build a 1-D-array
read -a line < "$1" # read the headline
COLS=${#line[#]} # save number of columns
index=0
while read -a line; do
for (( COUNTER=0; COUNTER<${#line[#]}; COUNTER++ )); do
array[$index]=${line[$COUNTER]}
((index++))
done
done < "$1"
for (( ROW = 0; ROW < COLS; ROW++ )); do
for (( COUNTER = ROW; COUNTER < ${#array[#]}; COUNTER += COLS )); do
printf "%s" ${array[$COUNTER]}
if [ $COUNTER -lt $(( ${#array[#]} - $COLS )) ]
then
printf "\t"
fi
done
printf "\n"
done
I was just looking for similar bash tranpose but with support for padding. Here is the script I wrote based on fgm's solution, that seem to work. If it can be of help...
#!/bin/bash
declare -a array=( ) # we build a 1-D-array
declare -a ncols=( ) # we build a 1-D-array containing number of elements of each row
SEPARATOR="\t";
PADDING="";
MAXROWS=0;
index=0
indexCol=0
while read -a line; do
ncols[$indexCol]=${#line[#]};
((indexCol++))
if [ ${#line[#]} -gt ${MAXROWS} ]
then
MAXROWS=${#line[#]}
fi
for (( COUNTER=0; COUNTER<${#line[#]}; COUNTER++ )); do
array[$index]=${line[$COUNTER]}
((index++))
done
done < "$1"
for (( ROW = 0; ROW < MAXROWS; ROW++ )); do
COUNTER=$ROW;
for (( indexCol=0; indexCol < ${#ncols[#]}; indexCol++ )); do
if [ $ROW -ge ${ncols[indexCol]} ]
then
printf $PADDING
else
printf "%s" ${array[$COUNTER]}
fi
if [ $((indexCol+1)) -lt ${#ncols[#]} ]
then
printf $SEPARATOR
fi
COUNTER=$(( COUNTER + ncols[indexCol] ))
done
printf "\n"
done
I was looking for a solution to transpose any kind of matrix (nxn or mxn) with any kind of data (numbers or data) and got the following solution:
Row2Trans=number1
Col2Trans=number2
for ((i=1; $i <= Line2Trans; i++));do
for ((j=1; $j <=Col2Trans ; j++));do
awk -v var1="$i" -v var2="$j" 'BEGIN { FS = "," } ; NR==var1 {print $((var2)) }' $ARCHIVO >> Column_$i
done
done
paste -d',' `ls -mv Column_* | sed 's/,//g'` >> $ARCHIVO
If you only want to grab a single (comma delimited) line $N out of a file and turn it into a column:
head -$N file | tail -1 | tr ',' '\n'
Not very elegant, but this "single-line" command solves the problem quickly:
cols=4; for((i=1;i<=$cols;i++)); do \
awk '{print $'$i'}' input | tr '\n' ' '; echo; \
done
Here cols is the number of columns, where you can replace 4 by head -n 1 input | wc -w.
Another awk solution and limited input with the size of memory you have.
awk '{ for (i=1; i<=NF; i++) RtoC[i]= (RtoC[i]? RtoC[i] FS $i: $i) }
END{ for (i in RtoC) print RtoC[i] }' infile
This joins each same filed number positon into together and in END prints the result that would be first row in first column, second row in second column, etc.
Will output:
X row1 row2 row3 row4
column1 0 3 6 9
column2 1 4 7 10
column3 2 5 8 11
#!/bin/bash
aline="$(head -n 1 file.txt)"
set -- $aline
colNum=$#
#set -x
while read line; do
set -- $line
for i in $(seq $colNum); do
eval col$i="\"\$col$i \$$i\""
done
done < file.txt
for i in $(seq $colNum); do
eval echo \${col$i}
done
another version with set eval
Here is a Bash one-liner that is based on simply converting each line to a column and paste-ing them together:
echo '' > tmp1; \
cat m.txt | while read l ; \
do paste tmp1 <(echo $l | tr -s ' ' \\n) > tmp2; \
cp tmp2 tmp1; \
done; \
cat tmp1
m.txt:
0 1 2
4 5 6
7 8 9
10 11 12
creates tmp1 file so it's not empty.
reads each line and transforms it into a column using tr
pastes the new column to the tmp1 file
copies result back into tmp1.
PS: I really wanted to use io-descriptors but couldn't get them to work.
Another bash variant
$ cat file
XXXX col1 col2 col3
row1 0 1 2
row2 3 4 5
row3 6 7 8
row4 9 10 11
Script
#!/bin/bash
I=0
while read line; do
i=0
for item in $line; { printf -v A$I[$i] $item; ((i++)); }
((I++))
done < file
indexes=$(seq 0 $i)
for i in $indexes; {
J=0
while ((J<I)); do
arr="A$J[$i]"
printf "${!arr}\t"
((J++))
done
echo
}
Output
$ ./test
XXXX row1 row2 row3 row4
col1 0 3 6 9
col2 1 4 7 10
col3 2 5 8 11
I'm a little late to the game but how about this:
cat table.tsv | python -c "import pandas as pd, sys; pd.read_csv(sys.stdin, sep='\t').T.to_csv(sys.stdout, sep='\t')"
or zcat if it's gzipped.
This is assuming you have pandas installed in your version of python
Here's a Haskell solution. When compiled with -O2, it runs slightly faster than ghostdog's awk and slightly slower than Stephan's thinly wrapped c python on my machine for repeated "Hello world" input lines. Unfortunately GHC's support for passing command line code is non-existent as far as I can tell, so you will have to write it to a file yourself. It will truncate the rows to the length of the shortest row.
transpose :: [[a]] -> [[a]]
transpose = foldr (zipWith (:)) (repeat [])
main :: IO ()
main = interact $ unlines . map unwords . transpose . map words . lines
An awk solution that store the whole array in memory
awk '$0!~/^$/{ i++;
split($0,arr,FS);
for (j in arr) {
out[i,j]=arr[j];
if (maxr<j){ maxr=j} # max number of output rows.
}
}
END {
maxc=i # max number of output columns.
for (j=1; j<=maxr; j++) {
for (i=1; i<=maxc; i++) {
printf( "%s:", out[i,j])
}
printf( "%s\n","" )
}
}' infile
But we may "walk" the file as many times as output rows are needed:
#!/bin/bash
maxf="$(awk '{if (mf<NF); mf=NF}; END{print mf}' infile)"
rowcount=maxf
for (( i=1; i<=rowcount; i++ )); do
awk -v i="$i" -F " " '{printf("%s\t ", $i)}' infile
echo
done
Which (for a low count of output rows is faster than the previous code).
A oneliner using R...
cat file | Rscript -e "d <- read.table(file('stdin'), sep=' ', row.names=1, header=T); write.table(t(d), file=stdout(), quote=F, col.names=NA) "
I've used below two scripts to do similar operations before. The first is in awk which is a lot faster than the second which is in "pure" bash. You might be able to adapt it to your own application.
awk '
{
for (i = 1; i <= NF; i++) {
s[i] = s[i]?s[i] FS $i:$i
}
}
END {
for (i in s) {
print s[i]
}
}' file.txt
declare -a arr
while IFS= read -r line
do
i=0
for word in $line
do
[[ ${arr[$i]} ]] && arr[$i]="${arr[$i]} $word" || arr[$i]=$word
((i++))
done
done < file.txt
for ((i=0; i < ${#arr[#]}; i++))
do
echo ${arr[i]}
done
Simple 4 line answer, keep it readable.
col="$(head -1 file.txt | wc -w)"
for i in $(seq 1 $col); do
awk '{ print $'$i' }' file.txt | paste -s -d "\t"
done
I have a long column of ones and zeroes:
0
0
0
1
0
0
0
0
0
1
0
0
0
0
0
1
0
0
1
....
I can easily get the average number of zeroes between ones (just total/ones):
ones=$(grep -c 1 file.txt)
lines=$(wc -l < file.txt)
echo "$lines / $ones" | bc -l
But how can I get the length of strings of zeroes between the ones? In the short example above it would be:
3
5
5
2
I'd include uniq for a more easily read approach:
uniq -c file.txt | awk '/ 0$/ {print $1}'
Edit: fixed for the case where the last line is a 0
Easy in awk:
awk '/1/{print NR-prev-1; prev=NR;}END{if (NR>prev)print NR-prev;}'
Not so difficult in bash, either:
i=0
for x in $(<file.txt); do
if ((x)); then echo $i; i=0; else ((++i)); fi
done
((i)) && echo $i
Using awk, I would use the fact that a field with the value 0 evaluates as False:
awk '!$1{s++; next} {if (s) print s; s=0} END {if (s) print s}' file
This returns:
3
5
5
2
Also, note the END block to print any "remaining" zeroes appearing after the last 1.
Explanation
!$1{s++; next} if the field is not True, that is, if the field is 0, increment the counter. Then, skip to the next line.
{if (s) print s; s=0} otherwise, print the value of the counter and reset it, but just if it contains some value (to avoid printing 0 if the file starts with a 1).
END {if (s) print s} print the remaining value of the counter after processing the file, but just if it wasn't printed before.
If your file.txt is just a column of ones and zeros, you can use awk and change the record separator to "1\n". This makes each "record" a sequence of "0\n", and the count of 0's in the record is the length of the record divided by 2. Counts will be correct for leading and trailing ones and zeros.
awk 'BEGIN {RS="1\n"} { print length/2 }' file.txt
This seems to be pretty popular question today. Joining the party late, here is another short gnu-awk command to do the job:
awk -F '\n' -v RS='(1\n)+' 'NF{print NF-1}' file
3
5
5
2
How it works:
-F '\n' # set input field separator as \n (newline)
-v RS='(1\n)+' # set input record separator as multipled of 1 followed by newline
NF # execute the block if minimum one field is found
print NF-1 # print num of field -1 to get count of 0
Pure bash:
sum=0
while read n ; do
if ((n)) ; then
echo $sum
sum=0
else
((++sum))
fi
done < file.txt
((sum)) && echo $sum # Don't forget to output the last number if the file ended in 0.
Another way:
perl -lnE 'if(m/1/){say $.-1;$.=0}' < file
"reset" the line counter when 1.
prints
3
5
5
2
You can use awk:
awk '$1=="0"{s++} $1=="1"{if(s)print s;s=0} END{if(s)print(s)}'
Explanation:
The special variable $1 contains the value of the first field (column) of a line of text. Unless you specify the field delimiter using the -F command line option it defaults to a widespace - meaning $1 will contain 0 or 1 in your example.
If the value of $1 equals 0 a variable called s will get incremented but if $1 is equal to 1 the current value of s gets printed (if greater than zero) and re-initialized to 0. (Note that awk initializes s with 0 before the first increment operation)
The END block gets executed after the last line of input has been processed. If the file ends with 0(s) the number of 0s between the file's end and the last 1 will get printed. (Without the END block they wouldn't printed)
Output:
3
5
5
2
if you can use perl:
perl -lne 'BEGIN{$counter=0;} if ($_ == 1){ print $counter; $counter=0; next} $counter++' file
3
5
5
2
It actually looks better with awk same logic:
awk '$1{print c; c=0} !$1{c++}' file
3
5
5
2
My attempt. Not so pretty but.. :3
grep -n 1 test.txt | gawk '{y=$1-x; print y-1; x=$1}' FS=":"
Out:
3
5
5
2
A funny one, in pure Bash:
while read -d 1 -a u || ((${#u[#]})); do
echo "${#u[#]}"
done < file
This tells read to use 1 as a delimiter, i.e., to stop reading as soon as a 1 is encountered; read stores the 0's in the fields of the array u. Then we only need to count the number of fields in u with ${#u[#]}. The || ((${#u[#]})) is here just in case your file doesn't end with a 1.
More strange (and not fully correct) way:
perl -0x31 -laE 'say #F+0' <file
prints
3
5
5
2
0
It
reads the file with the record separator is set to character 1 the -0x31
with autosplit -a (splits the record into array #F)
and prints the number of elements in #F e.g. say #F+0 or could use say scalar #F
Unfortunately, after the final 1 (as record separator) it prints an empty record - therefore prints the last 0.
It is incorrect solution, showing it only as alternative curiosity.
Expanding erickson's excellent answer, you can say:
$ uniq -c file | awk '!$2 {print $1}'
3
5
5
2
From man uniq we see that the purpose of uniq is to:
Filter adjacent matching lines from INPUT (or standard input), writing
to OUTPUT (or standard output).
So uniq groups the numbers. Using the -c option we get a prefix with the number of occurrences:
$ uniq -c file
3 0
1 1
5 0
1 1
5 0
1 1
2 0
1 1
Then it is a matter of printing those the counters before the 0. For this we can use awk like: awk '!$2 {print $1}'. That is: print the second field if the field is 0.
The simplest solution would be to use sed together with awk, like this:
sed -n '$bp;/0/{:r;N;/0$/{h;br}};/1/{x;bp};:p;/.\+/{s/\n//g;p}' input.txt \
| awk '{print length}'
Explanation:
The sed command separates the 0s and creates output like this:
000
00000
00000
00
Piped into awk '{print length}' you can get the count of 0 for each interval:
Output:
3
5
5
2