extract or recode a gtf file based on a gene id list

Question

[berge2015]

Hi,

Does anyone here know how to extract lines from a gtf file using a list/subset of gene id obtained from the same gtf file? I basically want a 'recoded' (in vcf terminology) gtf file containing information for only those genes which I am interested in.

I tried awk awk 'FNR==NR {a[$0];next} {for (i in a) if (i~$1) print i}' and grep grep -Fwf but these have not yielded what I want. Thank you for your help.

[shenwei356]

can you please paste some sample data?

Answer 1

[shenwei356]

try the powerfull CSV/TSV toolkit csvtk, usage of csvtk grep

csvtk grep -H -t -f 1 -r -P gene_id_list.txt ref_CDS.gtf

you may change the column index -f 1 where the gene id locates

Answer 2

[berge2015]

After playing with awk for a while, I came up with a solution: awk -F'"' 'FNR==NR {block[$0];next} $2 in block' gene_id_list.txt ref_CDS.gtf > out.txt [Note the quote delimeter]

While not the most elegant solution, this does what's asked in the question. Hope it helps anyone else looking for something similar.