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Questions and answers > RNA structures (DSSR)

List only base pairs in output

(1/1)

Llewellyn:
Is there a command to fetch only the base pairs in the output?

bp name
G-C WC
G-C WC
G-C WC
A-U WC
G-C WC
C-A --   
C-C --   
C-G WC
C-G WC
C-G WC
U-A WC
U-A WC
C-G WC
C-G WC
G-C WC
A-U WC       

xiangjun:
Try:

x3dna-dssr -i=1ehz.pdb --json | jq -c '.pairs[] | [.bp, .name]'

You would get:


--- Code: ---["G-C","WC"]
["C-G","WC"]
["G-C","WC"]
["G-U","Wobble"]
["A-U","WC"]
["U-A","WC"]
["U-A","WC"]
["U-A","rHoogsteen"]
["U+A","--"]
["A+A","--"]
["g-C","WC"]
["g+G","--"]
["C-G","WC"]
["U-A","WC"]
["C-G","WC"]
["G+C","rWC"]
["u+U","--"]
["G+P","--"]
["G-C","WC"]
["G-g","--"]
["g-A","Imino"]
["C-G","WC"]
["C-G","WC"]
["A-U","WC"]
["G-c","WC"]
["A-P","--"]
["c-A","--"]
["U-A","--"]
["c-G","WC"]
["U-A","WC"]
["G-C","WC"]
["U-A","WC"]
["G-C","WC"]
["t-a","rHoogsteen"]
--- End code ---

The jq utility program can be found on https://stedolan.github.io/jq/.

HTH,

Xiang-Jun

Llewellyn:
Thanks. It worked!

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Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.