extracting some part of a gtf file

Question

[zizigolu]

I have gtf file containing 7 columns from which i am going extract only gene name part from column 7th.

The 7th column contains some information including gene_id, gene_name and so on that I posted one row of column 7th below:

gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "NAC001"; oId "AT1G01010.1"; nearest_ref "AT1G01010.1"; class_code "="; tss_id

I need only gene_name from this column, for example "NAC001", how can I extract which I need please?

Answer 1

[GenoMax]

Sorry I missed the part that you only posted column 7 from your file. Either use @dschika's solution below or cut the 7th column and then use the one liner below.

$ awk -F ";" '{sub(/gene_name/,""); print $4}' your_file

If you don't need the quotes around the gene name

$ awk -F ";" '{sub(/gene_name/,""); print $4}' your_file | sed 's/"//g'

[zizigolu]

thank you

your code extracted what I need in cmd, but how I can write the result in a txt file?

[GenoMax]

Redirect the output to a new file with >. See my note above.

[zizigolu]

thank you very much for your quick and worth help

Answer 2

[dschika]

Assuming the fields in your gtf are tab separated you could try something like this:

awk 'BEGIN{FS="\t"}{print $7}' YOURFILE | awk 'BEGIN{FS="gene_name"}{print $2}' | awk 'BEGIN{FS=";"}{print $1}' > OUTFILE

genomax2 solution with sub is nicer.