find and replace one number with another

Question

I have created a 0,1,2 genotype matrix and I want to replace all of the -1 with 9.

0   0   -1  0   0   0   0   2   0   0   0   0   -1
0   0   1   0   0   0   0   0   0   0   0   -1   1
0   0   2   0   0   -1  2   0   0   0   -1  0    0

I tried this:

sed -ie 's/^[-1] /9 /' file1 > file2

but it seems that it does not work.

Is there any way to do that?

Answer 1

sed 's/-1/9/g' file > file2

Answer 2

sed -i 's/-1/9 /g' file
sed 's/-1/9 /g' file1 > file2

Answer 3

To do it in safe manner:

sed -e '
   s/$/ /
   :a;s/ -1 / 9 /;ta
   s/.$//
' file1

where

• s/$/ / insert a space at end of line
• :a;s/ -1 / 9 /;ta do substitution (space is needed if -1 at end of line)
• s/.$// remove space from end of line

Answer 4

I found the answer

sed -E 's/[-1] / 9/' file1 > file2

can do the job