easy way to fetch out the surrounding CDS of a pair of given coordinates
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5 weeks ago
zhangdengwei ▴ 150

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.

GFF • 244 views
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I finally succumb to coding by myself. The biopython module and pandas package can be helpful when doing such a thing.

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5 weeks ago
Juke34 ★ 6.3k

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

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