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
•
written
by
M K
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 $line genes.gtf; done < gene_names > gene_names.gtf
This will be a bit slower but does the job. If you want a super fast program, you may need to wait for a perl/Python script.
•
written
by
GouthamAtla
Hi Geek,
Komal helped me by using the following awk command
awk '{
for (i = 1; I <= NF; i++) {
if ($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.
M K I have replied to you on the previous question. Also, do not duplicate your posts.
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written
by
komal.rathi
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.
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