1

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?

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  • 2
    The [] enclose a collection of characters, so each occurrence of either - or 1 matches, but the ^ anchors the expression to the beginning of the line, so you don't get any match. You also miss the g flag to handle multiple occurences in a line. – Philippos Aug 3 '17 at 7:08
2
sed 's/-1/9/g' file > file2
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  • Place a space behind the 9 or you'll break the columns. – Philippos Aug 3 '17 at 7:09
1
sed -i 's/-1/9 /g' file
sed 's/-1/9 /g' file1 > file2
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0

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
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-2

I found the answer

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

can do the job

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