Change pattern just in next column matching another pattern - awk

Question

This is the header of my file:
1 HAVANA gene 11869 14409 . + . gene_name "DDX11L1" remap_original_location "chr1:+:11869-14409"
1 HAVANA gene 118569 148409 . + . gene_name "ORF21" remap_original_location "chr1:+:118569-148409" clinSig 0.59
1 HAVANA transcript 118568 148419 . + . remap_original_location "chr1:+:118568-148419" clinSig 0.02 M .
MT HAVANA gene 226 399 . + . remap_original_location "chrM:+:226-399" * + 3
MT HAVANA * 27 . -
I would like to save to another file exactly the same content than this, but just removing the chr pattern and transforming M to MT pattern in the column next to the column matching remap_original_location.
So, my desired output is:
1 HAVANA gene 11869 14409 . + . gene_name "DDX11L1" remap_original_location "1:+:11869-14409"
1 HAVANA gene 118569 148409 . + . gene_name "ORF21" remap_original_location "1:+:118569-148409" clinSig 0.59
1 HAVANA transcript 118568 148419 . + . remap_original_location "1:+:118568-148419" clinSig 0.02 M .
MT HAVANA gene 226 399 . + . remap_original_location "MT:+:226-399" * + 3
MT HAVANA * 27 . -
Do you know how can I achieve this?
I am trying some code like this:
awk '{for(i=1;i<=NF;i++){ if($i=="remap_original_location"){print ??? }}}'
But I am not sure how to specify the print part. In addition, as you can see, not all rows present the pattern remap_original_location and yet I still want to prin them.

Answer 1

With perl:
perl -pe 's/remap_original_location "\Kchr(M)?/$1 ? "MT" : ""/e' ip.txt
remap_original_location " I'm assuming single space to be consistent between fields here and that the next field will always start with " character. You can adjust the regex for other variations if needed
\K preceding portion won't be part of the matched text to be replaced
(M)? optionally match M character
$1 ? "MT" : "" if first capture group isn't empty, use MT as replacement string, else use empty string
empty string is Falsy in Perl
you can also use $1 && "MT" instead of ternary expression in this case, since the Falsy value is same as the alternate value needed
e flag helps to use Perl code in replacement section

Answer 2

You may use this awk:
awk '{gsub(/chr/, ""); for (i=1; i<NF; ++i) if ($i == "remap_original_location") {gsub(/M/, "MT", $(i+1)); break}} 1' file
1 HAVANA gene 11869 14409 . + . gene_name "DDX11L1" remap_original_location "1:+:11869-14409"
1 HAVANA gene 118569 148409 . + . gene_name "ORF21" remap_original_location "1:+:118569-148409" clinSig 0.59
1 HAVANA transcript 118568 148419 . + . remap_original_location "1:+:118568-148419" clinSig 0.02 M .
MT HAVANA gene 226 399 . + . remap_original_location "MT:+:226-399" * + 3
MT HAVANA * 27 . -
A more readable form:
awk '{
gsub(/chr/, "")
for (i=1; i<NF; ++i)
if ($i == "remap_original_location") {
gsub(/M/, "MT", $(i+1))
break
}
} 1' file

Answer 3

With your shown samples, could you please try following.
awk '
{
gsub(/chr/,"")
}
match($0,/remap_original_location "M:/){
val=substr($0,RSTART,RLENGTH)
sub(/"M:/,"\"MT:",val)
$0=substr($0,1,RSTART-1) val substr($0,RSTART+RLENGTH)
}
1' Input_file
OR as per Sundeep's comment one could try following too:
awk '{gsub(/chr/,""); sub(/remap_original_location "M/, "&T")} 1' Input_file