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I have the following data they are tab spaced but I discovered that some columns are not. How to make sure that the data are all tab spaced ?

here is part of the data:

rs987435    C   G   1   1   2   1   20
rs345783    C   G   1   1   1   1   01
rs955894    G   T   2   2   2   2   22
rs6088791   A   G   1   0   1   0   22
rs11180435  C   T   1   1   1   1   10
rs17571465  A   T   2   2   2   2   22
rs17011450  C   T   2   2   1   2   22
rs6919430   A   C   2   2   2   2   22
rs2342723   C   T   0   0   0   0   01
rs11992567  C   T   2   2   2   2   22

The columns starting from the 4th column should be 0,1,2 only; as you can see that the 8th column is not. I need to add tab between those numbers, how can I do that in Linux?

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2 Answers 2

Reset to default
2

Since you're using Linux you will have GNU Sed (as opposed to BSD Sed), and so you could simply do:

sed 's/.$/\t&/' file.txt

When satisfied with the output you see on the command line, do it "in place" (i.e. save it back to the file) with the -i flag:

sed -i 's/.$/\t&/' file.txt

What this does is insert a tab character before the final character on each line.

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  • Or use ed, which can do the in-place editing portably just fine. Commented Dec 11, 2016 at 23:24
  • @JdeBP, well, you could also include a literal tab character in the Sed replacement string to have it be portable, but they're annoying to type (can't be copy-pasted, can't be visually confirmed to be correct). I don't see that ed or ex has a portable way to specify a tab in the replacement string, either. Commented Dec 11, 2016 at 23:31
  • The non-portable part is not the tab character, which can be given to ed easily enough (it being a mistake to think that one needs special support from ed itself for it), but the -i option for the stream editor. Commented Dec 12, 2016 at 8:26
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Replace all spaces with tabs:

tr -s " " "\t" < datafile
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  • 1
    That doesn't actually answer the question. Look at the example text more carefully. Commented Dec 11, 2016 at 22:59

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