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Questions and answers => RNA structures (DSSR) => Topic started by: Llewellyn on July 26, 2018, 12:41:16 pm

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Title: List only base pairs in output
Post by: Llewellyn on July 26, 2018, 12:41:16 pm

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       

Title: Re: List only base pairs in output
Post by: xiangjun on July 26, 2018, 01:32:12 pm

Try:

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

You would get:

Code: [Select]

["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"]
The jq (https://stedolan.github.io/jq/) utility program can be found on https://stedolan.github.io/jq/.

HTH,

Xiang-Jun

Title: Re: List only base pairs in output
Post by: Llewellyn on July 26, 2018, 01:41:41 pm

Thanks. It worked!

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University