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I have a file which looks like this:

chr1 HAVANA exon 12613 12721 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1 HAVANA exon 13221 14409 . + . gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

I want to extract gene_id and gene_name values along with first 8 columns(file is tab separated). I have written a script in perl which can do this, but I am looking for a one liner in awk,sed etc which can do this.

PS. The file is tab separated and has 9 columns. The 9 th column has values which are separated by spaces.

My output should look like this:

chr1 HAVANA exon 12613 12721 . + . ENSG00000223972.5 DDX11L1
chr1 HAVANA exon 13221 14409 . + . ENSG00000223972.5 DDX11L1

awk ' print $1 "t" $2 "t" $3 "t" $4 "t" $5 "t" $6 "t" $7 "t" $8 "t" $10 "t" $16 ; ' filename > output

without quotes and semicolons :

awk ' print $1 "t" $2 "t" $3 "t" $4 "t" $5 "t" $6 "t" $7 "t" $8 "t" $10 "t" $16 ; ' filename | sed -e 's/;//g; s/"//g;' > output

more accurate using only awk:

awk ' ORS=" "; print $1 "t" $2 "t" $3 "t" $4 "t" $5 "t" $6 "t" $7 "t" $8 "t"; gsub(";", "", $10); gsub(""", "", $10); print $10 "t"; gsub(";", "", $16) ; gsub(""", "", $16); print $16 ; ORS="n" ; print " "; ' filename > output

Perl one-liner. It can be golfed a bit shorter, but I think this is pretty clear.

perl -F't' -lane '
 if (($id, $name) = / b gene_id s+ " ([^"]+) .+ b gene_name s+ " ([^"]+)/x) 
 print join "t", @F[0..7], $id, $name;
 
' file

A little more "clever":

perl -F't' -E '$,="t"; say @F[0..7], $gid, $gname if %g = /bgene_(id|name)s+"([^"]+)/g' file

The following awk script assumes that the 9th column could have data in any order.

The code will split the column on ; followed by an optional space. It will then iterate over the resulting elements and split these on spaces into a key value pair. If the key (the thing to the left of the space) is any of the two strings gene_id or gene_name, the value for this key is remembered. The parsing of the 9th column ends when we have found our two strings, after which the column is rewritten and the modified line is printed.

The code also discards any input that does not contain both gene_id and gene_name.

BEGIN 
 FS = OFS = "t"



 n = split($9, a, "; ?")

 found = 0;
 for (i = 1; i <= n; ++i)
 if (split(a[i], b, " ") == 2) 
 if (b[1] == "gene_id") 
 gene_id = b[2]
 ++found
 else if (b[1] == "gene_name") 
 gene_name = b[2]
 ++found
 

 if (found == 2) break
 

 if (found == 2) 
 $9 = gene_id " " gene_name
 print
 

Testing on the data provided:

$ awk -f script.awk <file
chr1 HAVANA exon 12613 12721 . + . "ENSG00000223972.5" "DDX11L1"
chr1 HAVANA exon 13221 14409 . + . "ENSG00000223972.5" "DDX11L1"

To remove the double quotes from the values, change

if (found == 2) 
 $9 = gene_id " " gene_name
 print

into

if (found == 2) 
 gsub(""", "", gene_id)
 gsub(""", "", gene_name)
 $9 = gene_id " " gene_name
 print

which removes all double quotes from the gene name and ID, or,

if (found == 2) 
 gene_id = substr(gene_id, 2, length(gene_id) - 2)
 gene_name = substr(gene_name, 2, length(gene_name) - 2)
 $9 = gene_id " " gene_name
 print

which removes the first and last characters from the two values.