easy way to fetch out the surrounding CDS of a pair of given coordinates

Question

[zhangdengwei]

Hi all,

I have a bacteria genome and the corresponding GFF annotation. Now I have a pair of coordinates and am wondering whether there is a quick way to fish out the surrounding CDS from the GFF file. Thanks in advance.

[zhangdengwei]

I finally succumb to coding by myself. The biopython module and pandas package can be helpful when doing such a thing.

Answer 1

[Juke34]

agat_sp_filter_record_by_coordinates.pl from AGAT for example.
Then you catch CDS with an awk command: awk '{if($3=="CDS"){print $0}}' my.gff