How to mach gene names and source (lincRNA, antisense, protein_coding,....) with specific list of genes id?

Question

[M K]

I have a list of gene id's and I want to match those with gene names and source (lincRNA, antisense, protein_coding, ...) from Ensembl gtf file. For example this is a small part of the list as shown:

Gene id             strand
ENSG00000242959     1
ENSG00000160396     -1
ENSG00000229494     1
ENSG00000230262     -1
ENSG00000229240     -1
ENSG00000223569     1

I got help before by using awk command to match gene id with gene name, so how can we include the source with them

Answer 1

[GouthamAtla]

Take only the column 1.

awk '{ print $1 }' input_list | sort | uniq > gene_names

Now take the gene names and grep against GTF file.

while read line; do grep $line genes.gtf; done < gene_names > gene_names.gtf

This will be a bit slower but does the job. If you want a super fast program, you may need to wait for a perl/Python script.

[M K]

Hi Geek,

Komal helped me by using the following awk command

awk '{                                
    for (i = 1; I <= NF; i++) {
        if ($i ~ /gene_id|gene_name/) {
            printf "%s ", $(i+1)
        }
    }
    print ""
}' Homo_sapiens.GRCh37.70.gtf | sed -e 's/"//g' -e 's/;//g' -e 's/ /\t/' | sort -k1,1 | uniq > Homo_sapiens.GRCh37.70.txt

and it works very well and I merged the result file with my file using R, So I wounder if we can add the source column in this command.

[komal.rathi]

M K I have replied to you on the previous question. Also, do not duplicate your posts.

Answer 2

[D. Puthier]

If looking for something more readable you may alternatively use gtftk the CLI of pygtftk. The gene_list.txt contains one column with any identifiers of interest related to the target key ("transcript_id" in your case)

 gtftk select_by_key -k transcript_id -f gene_list.txt -i genes.gtf -V 1   > gene_list.gtf

Best

Disclaimer: I'm the pygtftk developper.