Extract part of lines with specific pattern and store in a new field using awk or sed

Question

My problem is similar to this one, but the part I want to extract lies inside the line and I also want to store it in a newly created column in the original file rather than output.

A line in my tab-delimited file looks like:

chr1    25228613        25229157        CDS     HAVANA  .       -       2       ID=CDS:ENST00000338888.3;Parent=ENST00000338888.3;gene_id=ENSG00000020633.18_3;transcript_id=ENST00000338888.3_2;gene_type=protein_coding;gene_name=RUNX3;transcript_type=protein_coding;transcript_name=RUNX3-202;exon_number=7;exon_id=ENSE00001384103.2;level=2;protein_id=ENSP00000343477.3;transcript_support_level=1;tag=basic,appris_alternative_2,CCDS;ccdsid=CCDS30633.1;havana_gene=OTTHUMG00000003316.1_3;havana_transcript=OTTHUMT00000009285.1_2;remap_original_location=chr1:-:24902122-24902666;remap_status=full_contig

I want to extract content behind "gene_name" in $9, this line is RUNX3.

The expected output:

chr1    25228613        25229157        CDS     HAVANA  .       -       2       ID=CDS:ENST00000338888.3;Parent=ENST00000338888.3;gene_id=ENSG00000020633.18_3;transcript_id=ENST00000338888.3_2;gene_type=protein_coding;gene_name=RUNX3;transcript_type=protein_coding;transcript_name=RUNX3-202;exon_number=7;exon_id=ENSE00001384103.2;level=2;protein_id=ENSP00000343477.3;transcript_support_level=1;tag=basic,appris_alternative_2,CCDS;ccdsid=CCDS30633.1;havana_gene=OTTHUMG00000003316.1_3;havana_transcript=OTTHUMT00000009285.1_2;remap_original_location=chr1:-:24902122-24902666;remap_status=full_contig    RUNX3

How to do it using awk or sed?

Answer 1

Since you know the delimiters then just split and reassemble on those

sed -Ei 's/(.*gene_name=)([^;]*)(;.*)/\1\2\3\t\2/g' gene

which breaks down into

(.*gene_name=)

all of your string up to the gene_name tag goes into variable 1

([^;]*)

all continuous characters up to the ; go into variable 2

(;.*)

the rest of your string goes into variable 3

\1\2\3\t\2

recompose your string with a tab and the gene appended

EDIT

or as @Weijun notes

\0\t\2

Another EDIT

Code golfing

sed -Ei 's/.*gene_name=([^;]*).*/\0\t\1/g' gene

Answer 2

With gawk:

gawk 'match($9,/^.*gene_name=([^;]*);.*/,arr) {print $0"\t"arr[1]}'

This appends gene_name to the end of each line that contains the "gene_name=" string. You may fine tune it for your needs.

Answer 3

Following awk may also help you in same.

awk '{val=$0;sub(/.*gene_name=/,"",val);sub(/\;.*/,"",val);print $0,val}' Input_file

Answer 4

This is a generic awk solution to parsing out a specific named field out of the attributes field (the 9th tab-delimited field) of a file in the General Feature Format (GFF):

BEGIN { OFS = FS = "\t" }

function get_attrib_by_name(key,  n,attrib,kv) {
    # Split the attribute field on semi-colons.
    n = split($9, attrib, ";")

    # Loop over the attributes and split each on "=".
    # When we've found the one we're looking for (by key name in "key"),
    # return the corresponding value.
    for (i = 1; i <= n; ++i) {
        split(attrib[i], kv, "=")
        if (kv[1] == key) {
            return kv[2]
        }
    }
}

# Using the above function.
{
    name = get_attrib_by_name("gene_name")
    print $0, name
}

This would be used like

$ awk -f script.awk file.gff

where script.awk is the above script.