bplfile: Creates a bpl file from a coordinate file

In RRNA: Secondary Structure Plotting for RNA

Description

A bpl file can be created from a given coordinate file for inputing into other RNA visulatization programs

Usage

bplfile(dat, name)

Arguments

dat	Coordinate file created by ct2coord or loadCoords functions ct=makeCt("((((...))))","AAAACCCUUUU") ### Create the coordinate file ### dat=ct2coord(ct)
name	Name of the file outputed

Value

Creates the file with the given "name"

Author(s)

JP Bida

Examples

ct=makeCt("((((...))))","AAAACCCUUUU")
### Create the coordinate file ###
dat=ct2coord(ct)

bplfile(dat,"test.bpl")

Example output

   pos before after seq pos2 bound
2   12     11    13   A   12     0
21  13     12    14   A   13    -1
1    1      0     2   A    1    11
22   2      1     3   A    2    10
3    3      2     4   A    3     9
4    4      3     5   A    4     8
5    5      4     6   C    5     0
6    6      5     7   C    6     0
7    7      6     8   C    7     0
8    8      7     9   U    8     4
9    9      8    10   U    9     3
10  10      9    11   U   10     2
11  11     10    12   U   11     1
14   0     -1     1   A    0    12
15  -1     -2     0   A   -1    13
[1] "-1 13 0 0 0 1 -1 0"
$x
[1] -1

$y
[1] 0

[1] 1.047198
[1] "12 13 12"
[1] "11 12 11"
[1] "10 11 10"
[1] "9 10 9"
[1] "8 9 8"
[1] "New LOOPS:  c(4, 8)"
[1] 4

RRNA documentation built on May 2, 2019, 1:06 p.m.