awk - Replace all instances of - with . until A or G or T or C from both ends of a string -

so example if input is:

-------a--gg---ccaat---a------

output should be:

.......a--gg---ccaat---a......

prefer in awk.

this going bit complicated because awk not allow call function matched string, need manually take out matched strings (l , r), further process them, , replace $0 original string plus matched strings:

awk '{     if (match($0, /^-*/)) { l = substr($0, 1, rlength); gsub("-", ".", l); $0 = l substr($0, rlength + 1); }     if (match($0, /-*$/)) { r = substr($0, rstart); gsub("-", ".", r); $0 = substr($0, 1, rstart - 1) r; }     print $0; }' 

or using gsub again mutate matched strings in $0 instead of concatenating:

awk '{     if (match($0, /^-*/)) { l = substr($0, 1, rlength); gsub("-", ".", l); gsub(/^-*/, l, $0); }     if (match($0, /-*$/)) { r = substr($0, rstart); gsub("-", ".", r); gsub(/-*$/, r, $0); }     print $0; }'