1

What I would like to do is search for lines where the first column does not begin with 'rs' or 'chr' THEN if those lines begin with a number, append 'chr' to the first column value, otherwise leave as it was - no appending.

I have the following code:

awk '((!($1 ~ /rs/ || $1 ~ /chr/)) && $1 ~ /^[[:0-9:]]|$/) {$1 = "chr"$1}1' filename > newfilename

This is good but appends 'chr' to all first column values that do not begin with 'rs' or 'chr'. There are some values in this column that I do not want to change and these all begin with letters (a-z). I only want to change the values which start with numbers (0-9).

Thanks!

2

As already mentioned in the comments by Fiximan, looking for a digit automatically filters out 'rs' and 'chr'. So if you want to prepend lines starting with a digit with 'chr' you can do the following:

awk '{if ($1 ~ /^[:0-9:]/) printf "chr%s\n", $0; else printf "%s\n", $0;}' filename > newfile
0

using sed

sed 's/^[0-9]/chr&/' file

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