Convert protein name to letter e.g. p.Arg135Trp to p.R135W
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16 months ago
whb ▴ 30

How to convert snpeff output of protein change from p.Arg135Trp to p.R135W? so that I can import into maftools,

How can it be done in R or bash?

Thanks

aminoacid • 534 views
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python script available here for converting 3 to 1 and 1 and 3. User input is a single column file.

https://github.com/svsuresh/python_scripts/blob/master/hgvs_p_syntax_conversion.ipynb

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16 months ago
tothepoint ▴ 680

Create a text file with all the input (Your_file.txt) and this will help you to get the desired output.

sed 's/Ala/A/g;s/Cys/C/g;s/Asp/D/g;s/Glu/E/g;s/Phe/F/g;s/Gly/G/g;s/His/H/g;s/Hid/H/g;s/Hie/H/g;s/Ile/I/g;s/Lys/K/g;s/Leu/L/g;s/Met/M/g;s/Asn/N/g;s/Pro/P/g;s/Gln/Q/g;s/Arg/R/g;s/Ser/S/g;s/Thr/T/g;s/Val/V/g;s/Trp/W/g;s/Tyr/Y/g;s/Mse/X/g' < Your_file.txt > desired_output.txt
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