printing variable number lines to output - bash

I would like to have a script to modify some large text files (100k records) such that, for every record, a number of lines in the output is created equivalent to the difference in columns 3 and 2 of every input line. In the output I want to print the record name (column 1), and a step-wise walk between the numbers contained in columns 2 and 3.
Sample trivial input could be (tab separated data, if it makes a difference)
a 3 5
b 10 14
with the desired output (again, ideally tab separated)
a 3 4
a 4 5
b 10 11
b 11 12
b 12 13
b 13 14
It's a challenge sadly beyond my (very) limited abilities.
Can anyone provide a solution to the problem, or point me in the right direction? In an ideal world I would be able to be integrate this into a bash script, but I'll take anything that works!


Bash solution:
while read h f t ; do
for ((i=f; i<t; i++)) ; do
printf "%s\t%d\t%d\n" $h $i $((i+1))
done
done < input.txt
Perl solution:
perl -lape '$_ = join "\n", map join("\t", $F[0], $_, $_ + 1), $F[1] .. $F[2] - 1' input.txt


awk -F '\t' -v OFS='\t' '
$2 >= $3 {print; next}
{for (i=$2; i<$3; i++) print $1, i, i+1}
' filename


With awk:
awk '$3!=$2 { while (($3 - $2) > 1) { print $1,$2,$2+1 ; $2++} }1' inputfile


Fully POSIX, and no unneeded loop variables:
$ while read h f t; do
while test $f -lt $t; do
printf "%s\t%d\t%d\n" "$h" $f $((++f))
done
done < input.txt
a 3 4
a 4 5
b 10 11
b 11 12
b 12 13
b 13 14

Related

Print first few and last few lines of file through a pipe with "..." in the middle

Problem Description
This is my file
1
2
3
4
5
6
7
8
9
10
I would like to send the cat output of this file through a pipe and receive this
% cat file | some_command
1
2
...
9
10
Attempted solutions
Here are some solutions I've tried, with their output
% cat temp | (head -n2 && echo '...' && tail -n2)
1
2
...
% cat temp | tee >(head -n3) >(tail -n3) >/dev/null
1
2
3
8
9
10
# I don't know how to get the ...
% cat temp | sed -e 1b -e '$!d'
1
10
% cat temp | awk 'NR==1;END{print}'
1
10
# Can only get 2 lines

An awk:
awk -v head=2 -v tail=2 'FNR==NR && FNR<=head
FNR==NR && cnt++==head {print "..."}
NR>FNR && FNR>(cnt-tail)' file file
Or if a single pass is important (and memory allows), you can use perl:
perl -0777 -lanE 'BEGIN{$head=2; $tail=2;}
END{say join("\n", #F[0..$head-1],("..."),#F[-$tail..-1]);}' file
Or, an awk that is one pass:
awk -v head=2 -v tail=2 'FNR<=head
{lines[FNR]=$0}
END{
print "..."
for (i=FNR-tail+1; i<=FNR; i++) print lines[i]
}' file
Or, nothing wrong with being a caveman direct like:
head -2 file; echo "..."; tail -2 file
Any of these prints:
1
2
...
9
10
It terms of efficiency, here are some stats.
For small files (ie, less than 10 MB or so) all these are less than 1 second and the 'caveman' approach is 2 ms.
I then created a 1.1 GB file with seq 99999999 >file
The two pass awk: 50 secs
One pass perl: 10 seconds
One pass awk: 29 seconds
'Caveman': 2 MS

You may consider this awk solution:
awk -v top=2 -v bot=2 'FNR == NR {++n; next} FNR <= top || FNR > n-top; FNR == top+1 {print "..."}' file{,}
1
2
...
9
10

Two single pass sed solutions:
sed '1,2b
3c\
...
N
$!D'
and
sed '1,2b
3c\
...
$!{h;d;}
H;g'

Assumptions:
as OP has stated, a solution must be able to work with a stream from a pipe
the total number of lines coming from the stream is unknown
if the total number of lines is less than the sum of the head/tail offsets then we'll print duplicate lines (we can add more logic if OP updates the question with more details on how to address this situation)
A single-pass awk solution that implements a queue in awk to keep track of the most recent N lines; the queue allows us to limit awk's memory usage to just N lines (as opposed to loading the entire input stream into memory, which could be problematic when processing a large volume of lines/data on a machine with limited available memory):
h=2 t=3
cat temp | awk -v head=${h} -v tail=${t} '
{ if (NR <= head) print $0
lines[NR % tail] = $0
}
END { print "..."
if (NR < tail) i=0
else i=NR
do { i=(i+1)%tail
print lines[i]
} while (i != (NR % tail) )
}'
This generates:
1
2
...
8
9
10
Demonstrating the overlap issue:
$ cat temp4
1
2
3
4
With h=3;t=3 the proposed awk code generates:
$ cat temp4 | awk -v head=${h} -v tail=${t} '...'
1
2
3
...
2
3
4
Whether or not this is the 'correct' output will depend on OP's requirements.

I suggest with bash:
(head -n 2; echo "..."; tail -n 2) < file
Output:
1
2
...
9
10

Foreach command with table [duplicate]

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

Find a number of a file in a range of numbers of another file

I have this two input files:
file1
1 982444
1 46658343
3 15498261
2 238295146
21 47423507
X 110961739
17 7490379
13 31850803
13 31850989
file2
1 982400 982480
1 46658345 46658350
2 14 109
2 5000 9000
2 238295000 238295560
X 110961739 120000000
17 7490200 8900005
And this is my desired output:
Desired output:
1 982444
2 238295146
X 110961739
17 7490379
This is what I want: Find the column 1 element of file1 in column 1 of file2. If the number is the same, take the number of column 2 of file1 and check if it is included in the range of numbers of column2 and 3 of file2. If it is included, print the line of file1 in the output.
Maybe is a little confusing to understand, but I'm doing my best. I have tried some things but I'm far away from the solution and any help will be really appreciated. In bash, awk or perl please.
Thanks in advance,

Just using awk. The solution doesn't loop through file1 repeatedly.
#!/usr/bin/awk -f
NR == FNR {
# I'm processing file2 since NR still matches FNR
# I'd store the ranges from it on a[] and b[]
# x[] acts as a counter to the number of range pairs stored that's specific to $1
i = ++x[$1]
a[$1, i] = $2
b[$1, i] = $3
# Skip to next record; Do not allow the next block to process a record from file2.
next
}
{
# I'm processing file1 since NR is already greater than FNR
# Let's get the index for the last range first then go down until we reach 0.
# Nothing would happen as well if i evaluates to nothing i.e. $1 doesn't have a range for it.
for (i = x[$1]; i; --i) {
if ($2 >= a[$1, i] && $2 <= b[$1, i]) {
# I find that $2 is within range. Now print it.
print
# We're done so let's skip to the next record.
next
}
}
}
Usage:
awk -f script.awk file2 file1
Output:
1 982444
2 238295146
X 110961739
17 7490379
A similar approach using Bash (version 4.0 or newer):
#!/bin/bash
FILE1=$1 FILE2=$2
declare -A A B X
while read F1 F2 F3; do
(( I = ++X[$F1] ))
A["$F1|$I"]=$F2
B["$F1|$I"]=$F3
done < "$FILE2"
while read -r LINE; do
read F1 F2 <<< "$LINE"
for (( I = X[$F1]; I; --I )); do
if (( F2 >= A["$F1|$I"] && F2 <= B["$F1|$I"] )); then
echo "$LINE"
continue
fi
done
done < "$FILE1"
Usage:
bash script.sh file1 file2

Let's mix bash and awk:
while read col min max
do
awk -v col=$col -v min=$min -v max=$max '$1==col && min<=$2 && $2<=max' f1
done < f2
Explanation
For each line of file2, read the min and the max, together with the value of the first column.
Given these values, check in file1 for those lines having same first column and being 2nd column in the range specified by file 2.
Test
$ while read col min max; do awk -v col=$col -v min=$min -v max=$max '$1==col && min<=$2 && $2<=max' f1; done < f2
1 982444
2 238295146
X 110961739
17 7490379

Pure bash , based on Fedorqui solution:
#!/bin/bash
while read col_2 min max
do
while read col_1 val
do
(( col_1 == col_2 && ( min <= val && val <= max ) )) && echo $col_1 $val
done < file1
done < file2

cut -d' ' -f1 input2 | sed 's/^/^/;s/$/\\s/' | \
grep -f - <(cat input2 input1) | sort -n -k1 -k3 | \
awk 'NF==3 {
split(a,b,",");
for (v in b)
if ($2 <= b[v] && $3 >= b[v])
print $1, b[v];
if ($1 != p) a=""}
NF==2 {p=$1;a=a","$2}'
Produces:
X 110961739
1 982444
2 238295146
17 7490379

Here's a Perl solution. It could be much faster but less concise if I built a hash out of file2, but this should be fine.
use strict;
use warnings;
use autodie;
my #bounds = do {
open my $fh, '<', 'file2';
map [ split ], <$fh>;
};
open my $fh, '<', 'file1';
while (my $line = <$fh>) {
my ($key, $val) = split ' ', $line;
for my $bound (#bounds) {
next unless $key eq $bound->[0] and $val >= $bound->[1] and $val <= $bound->[2];
print $line;
last;
}
}
output
1 982444
2 238295146
X 110961739
17 7490379

How can I use awk to sort columns by the last value of a column?

I have a file like this (with hundreds of lines and columns)
1 2 3
4 5 6
7 88 9
and I would like to re-order columns basing on the last line values (or a specific line values)
1 3 2
4 6 5
7 9 88
How can I use awk (or other) to accomplish this task?
Thank you in advance for your help
EDIT: I would like to thank everybody and to apologize if I wasn't enough clear.
What I would like to do is:
take a line (for example the last one);
reorder the columns of the matrix using the sorted values of the chosen line to derermine the order.
So, the last line is 7 88 9, which sorted is 7 9 88, then the three columns have to be reordered in a way such that, in this case, the last two columns are swapped.
A four-column more generic example, based on the last line again:
Input:
1 2 3 4
4 5 6 7
7 88.0 9 -3
Output:
4 1 3 2
7 4 6 5
-3 7 9 88.0

Here's a quick, dirty and improvable solution: (edited because OP clarified that numbers are floating point).
$ cat test.dat
1 2 3
4 5 6
.07 .88 -.09
$ awk "{print $(printf '$%d%.0s\n' \
$(i=0; for x in $(tail -n1 test.dat); do
echo $((++i)) $x
done |
sort -k2g) | paste -sd,)}" test.dat
3 1 2
6 4 5
-.09 .07 .88
To see what's going on there (or at least part of it):
$ echo "{print $(printf '$%d%.0s\n' \
$(i=0; for x in $(tail -n1 test.dat); do
echo $((++i)) $x
done |
sort -k2g) | paste -sd,)}" test.dat
{print $3,$1,$2} test.dat
To make it work for an arbitrary line, replace tail -n1 with tail -n+$L|head -n1

This problem can be elegantly solved using GNU awk's array sorting feature. GNU awk allows you to control array traversal using PROCINFO. So two passes of the file are required, the first pass to split the last record into an array and the second pass to loop through the indices of the array in value order and output fields based on indices. The code below probably explains it better than I do.
awk 'BEGIN{PROCINFO["sorted_in"] = "#val_num_asc"};
NR == FNR {for (x in arr) delete arr[x]; split($0, arr)};
NR != FNR{sep=""; for (x in arr) {printf sep""$x; sep=" "} print ""}' file.txt file.txt
4 1 3 2
7 4 6 5
-3 7 9 88.0

Update:
Create a file called transpose.awk like this:
{
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 OFS a[i,j];
}
print str
}
}
Now here is the script that should do work for you:
awk -f transpose.awk file | sort -n -k $(awk 'NR==1{print NF}' file) | awk -f transpose.awk
1 3 2
4 6 5
7 9 88
I am using transpose.awk twice here. Once to transpose rows to columns then I am doing numeric sorting by last column and then again I am transposing rows to columns. It may not be most efficient solution but it is something that works as per the OP's requirements.
transposing awk script courtesy of: #ghostdog74 from An efficient way to transpose a file in Bash

Add leading zeroes to awk variable

I have the following awk command within a "for" loop in bash:
awk -v pdb="$pdb" 'BEGIN {file = 1; filename = pdb"_" file ".pdb"}
/ENDMDL/ {getline; file ++; filename = pdb"_" file ".pdb"}
{print $0 > filename}' < ${pdb}.pdb
This reads a series of files with the name $pdb.pdb and splits them in files called $pdb_1.pdb, $pdb_2.pdb, ..., $pdb_21.pdb, etc. However, I would like to produce files with names like $pdb_01.pdb, $pdb_02.pdb, ..., $pdb_21.pdb, i.e., to add padding zeros to the "file" variable.
I have tried without success using printf in different ways. Help would be much appreciated.

Here's how to create leading zeros with awk:
# echo 1 | awk '{ printf("%02d\n", $1) }'
01
# echo 21 | awk '{ printf("%02d\n", $1) }'
21
Replace %02 with the total number of digits you need (including zeros).

Replace file on output with sprintf("%02d", file).
Or even the whole assigment with filename = sprintf("%s_%02d.pdb", pdb, file);.

This does it without resort of printf, which is expensive. The first parameter is the string to pad, the second is the total length after padding.
echo 722 8 | awk '{ for(c = 0; c < $2; c++) s = s"0"; s = s$1; print substr(s, 1 + length(s) - $2); }'
If you know in advance the length of the result string, you can use a simplified version (say 8 is your limit):
echo 722 | awk '{ s = "00000000"$1; print substr(s, 1 + length(s) - 8); }'
The result in both cases is 00000722.

Here is a function that left or right-pads values with zeroes depending on the parameters: zeropad(value, count, direction)
function zeropad(s,c,d) {
if(d!="r")
d="l" # l is the default and fallback value
return sprintf("%" (d=="l"? "0" c:"") "d" (d=="r"?"%0" c-length(s) "d":""), s,"")
}
{ # test main
print zeropad($1,$2,$3)
}
Some tests:
$ cat test
2 3 l
2 4 r
2 5
a 6 r
The test:
$ awk -f program.awk test
002
2000
00002
000000
It's not fully battlefield tested so strange parameters may yield strange results.

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