centroid_bpp.py

• Author: Soh Ishiguro

centroid_bpp.py is tiny command line tool that allow us to show base-pair probability each base position from given bppm file. Input bppm file is generated by following command:

centroid_fold --posteriors 0.0001 --oposteriors out.bppm --postscript out.ps -o out.out out.fa

Usage

• python centroid_bpp.py --help # show help messages.
• python centroid_bpp.py --file example.bppm > out.log

out.log has base-pair probability per base, then you can plot of this distribution by simple R code.

library(ggplot2)
d <- read.csv("test.log", header=F)
names(d) <- c("pos", "prob")
ggplot(d, aes(x=pos, y=prob)) + geom_line(colour="brown2", size=1) + theme_classic() + labs(y="Base-pair probability", x="position")