file transposing

Shell Programming and Scripting
1

Hello,

Is there a way to transpose a file in shell scripting? For instance, from

a1 a2 a3 a4 a5 a6 a7 ....
b1 b2 b3 b4 b5 b6 b7 ....
c1 c2 c3 c4 c5 c6 c7 ....
d1 d2 d3 d4 d5 d6 d7 ...
...
...
...

to

a1 b1 c1 d1 ....
a2 b2 c2 d2 ....
a3 b3 c3 d3 ....
a4 b3 c3 d4 ....
...
...
...

Thanks in advance.

2

Yes there is, the question has been answered here several times. Try using the search functionality with keywords "row", "column" and "transpose".

3

Try...

awk '{
      for (f = 1; f <= NF; f++)
         a[NR, f] = $f
   }
   NF > nf { nf = NF }
   END {
      for (f = 1; f <= nf; f++)
         for (r = 1; r <= NR; r++)
            printf a[r, f] (r==NR ? RS : FS)
   }' file1 > file2
4

Thanks, but the code didn't work. Any idea? why

5

no, not from your description - works fine here.

6

Wired, My file is a multi-column based tab delimited file with uneven rows. It needs to be transposed to row based txt file. This is code,
bash-2.03$ more file_transpose
###file transpose, colume to row
###from Unix Linux Community - Technical support for all Unix and Linux users, 07/29/2005

awk '{
for (f = 1; f <= NF; f++)
a[NR, f] = $f
}
NF > nf { nf = NF }
END {
for (f = 1; f <= nf; f++)
for (r = 1; r <= NR; r++)
printf a[r, f] (r==NR ? RS : FS)
}' atcc_fidler_pvs_all_markers.txt > atcc_fidler_pvs_all_markers_out.txt

The error message is,
sorgerlab-x% bash
bash-2.03$ ./file_transpose
awk: syntax error near line 3
awk: illegal statement near line 3
awk: syntax error near line 9
awk: illegal statement near line 9

Thanks for the help

7

by the way, how to search the archives here.

8

If on Solaris, try using 'nawk' instead of plain 'awk'

9

by clicking the 'Search' and filling in the drop-down menu.

10

Using Ruby:

[[1,2,3], [4,5,6]].transpose

yields

[[1, 4], [2, 5], [3, 6]]

11

Thank you guys. It worked by change awk to nawk, but the output is not tab delimited format. Can anyone fix it for me? thx.

12

nawk -v OFS='\t' ..........

13

Thanks! It worked well. But if I need to transpose a file like this to a colume based file, how can I do it? Please help. Thanks in advance.

14

can you elaborate on the question, pls?

15

Thanks. The problem is somehow just a opposite of the original one. Basically, we need to transpose a row based file to a column based file, please see below. Since the Excel has a limitation of 256 columns, it is almost useless to those who want to transpose a big file.

file format(tab delimited):

chip1 a1 b1 c1 d1 ......
chip2 a2 b2 c2 d2 .............
chip3 a3 b3 c3 d3 .........
....

after transpose(tab delimited),
chip1 chip2 chip3 chip4 ...
a1 b1 c1 d1 ...
a2 b2 c2 d2 ...
a3 b3 c3 d3 ...
....

16

sorry, it's wrong.
after transpose,

chip1 chip2 chip3 ...
a1 a2 a3 ...
b1 b2 b3 ...
c1 c2 c3 ...
....

17

how's that different from the original?
the output I get is:

chip1   chip2   chip3
a1      a2      a3
b1      b2      b3
c1      c2      c3
d1      d2      d3
18

original was column to row, but now is row to column.

19

have you tried running the script?
isn't the above output what you wanted?

20

yes, original input was,
chip1 chip2 chip3 ...
a1 a2 a3 ...
b1 b2 b3 ...
c1 c2 c3 ...
...

output was,
chip1 a1 b1 c1 ...........
chip2 a2 b2 c2 ......
chip3 a3 b3 c3 ..............
...