ct2knet: creates a knet file from a CT file

In jpbida/RRNA: Secondary Structure Plotting for RNA

creates a knet file from a CT file

Description

Knet files are used as inputs for KnetFold secondary structure prediction program

Usage

ct2knet(file, ind = 0)

Arguments

file	Name of the CT file being converted to KnetFold file
ind	Index used to relabel sequence indexes

Value

Retuns a string containing the contains of the knet file

Author(s)

JP Bida

Examples

pk=makeCt("((((...(((((((.........)))))))...((((.........))))...))))",
          "AAAAAAAACCCCCCCCAAAGGGGGGGAUUACCCCUCCUUUAAAAGGGUUUUCCCCCCC"
         )
pk$bound[pk$pos==20]=42
pk$bound[pk$pos==19]=43
pk$bound[pk$pos==43]=19
pk$bound[pk$pos==42]=20

### Create a CT file for testing ###
ctfile = tempfile(fileext=".ct")
write.table(pk[,c(1,4,2,3,6,5)],file=ctfile,row.names=FALSE,col.names=TRUE)

### Convert CT file to Knet ###
out=ct2knet(ctfile,0)

jpbida/RRNA documentation built on April 28, 2024, 1:27 p.m.