How to add double quotes around string and number pattern?

Hi I need to add double quotes in a pattern in 300k lines. I'm trying to use sed and I read multiple inquiries here and other sources, but I can't seem to understand its syntax.

I have:

chr1    StringTie       exon    191964  192299  1000    -       .       gene_id MSTRG.201; transcript_id MSTRG.201.53; exon_number 2;
chrY    StringTie       exon    26420508        26420531        1000    +       .       gene_id MSTRG.49889; transcript_id MSTRG.49889.11; exon_number 1;

And I need to have:

chr1    StringTie       exon    191964  192299  1000    -       .       gene_id "MSTRG.201"; transcript_id "MSTRG.201.53"; exon_number 2;
chrY    StringTie       exon    26420508        26420531        1000    +       .       gene_id "MSTRG.49889"; transcript_id "MSTRG.49889.11"; exon_number 1;

I'm using sed as follows:

sed 's/MSTRG./"MSTRG."/g' filename

But I can only get:

chr1    StringTie       exon    191964  192299  1000    -       .       gene_id "MSTRG."201; transcript_id "MSTRG."201.53; exon_number 2;
chrY    StringTie       exon    26420508        26420531        1000    +       .       gene_id "MSTRG."49889; transcript_id "MSTRG."49889.11; exon_number 1;

I've tried:

sed -Ei 's|MSTRG[[:digit:]]+|"&"|g' filename
sed 's/M/"M/; s/$/"/' filename
sed 's/MSTRG.[[:digit:]]+/"MSTRG.[[:digit:]]+"/g' filename

But none of these will work.

I was wondering if I could use awk, but I don't have any skills in this language.

Any help, please?

Thanks in advance.

Why limit yourself to this particular gene name? Here's a more general solution that will put anything after gene_id or transcript_id and until the first ; in quotes:

$ sed -E 's/(transcript_id|gene_id)  *([^;]+)/\1 "\2"/g' file
chr1    StringTie       exon    191964  192299  1000    -       .       gene_id "MSTRG.201"; transcript_id "MSTRG.201.53"; exon_number 2;
chrY    StringTie       exon    26420508        26420531        1000    +       .       gene_id "MSTRG.49889"; transcript_id "MSTRG.49889.11"; exon_number 1;

Explanation

• -E: this enables extended regular expressions which let us use ( ) unescaped (not \( \)) to capture groups, and also gives us + for "one or more" and allows us to use unescaped | for "either this or that".
• s/(transcript_id|gene_id) *([^;]+)/\1"\2"/g': we are looking for either transcript_id or gene_id (that's why the | is used, for "OR"), followed by one or more spaces ( +), and then one or more non-; characters. The parentheses are used to capture what is matched, so it can then be used on the right hand side of the substitution operator. The first captured group (here, the transcript_id or gene_id along with the spaces) will be \1, the second will be \2 and so on. Then, this is all replaced with whatever was captured first (\1) and then whatever was captured second, surrounded by quotes ("\2").
• s///g: the g is needed to make the substitution global, to substitute all matches found on the same line. Without the g, only the first match would be substituted.

You can use this on arbitrary gene names, even an entire GTF file and it should work just fine.

With GNU sed:

sed -E 's/MSTRG[0-9.]+/"&"/g' file

Output:

chr1    StringTie       exon    191964  192299  1000    -       .       gene_id "MSTRG.201"; transcript_id "MSTRG.201.53"; exon_number 2;
chrY    StringTie       exon    26420508        26420531        1000    +       .       gene_id "MSTRG.49889"; transcript_id "MSTRG.49889.11"; exon_number 1;

&: refer to that portion of the pattern space which matched

See: man sed and The Stack Overflow Regular Expressions FAQ