Delila Program: rila

# rila program

## This program is part of the Individual Information theory software package. The patent is now expired and the program is available. By downloading this code you agree to the Source Code Use License (PDF). Pascal source code: rila.p (wget instructions) Instructions on compiling MacOS binary: rila Alphabetic List of Delila Programs Delila Programs by Most Recent Update Please report broken links delilabundle.zip = All Programs and MacOS Binaries Copyright Statement for Delila Programs

### Documentation for the rila program is below, with links to related programs in the "see also" section.

{   version = 1.43; (* of rila.p 2013 Mar 12}

(* begin module describe.rila *)
(*
name
rila: reformat the ribl table into latex format

synopsis
rila(ribl: in, rilap: in,
headlatex: out, labelatex: out, senulatex: out,
sequlatex: out, freqlatex: out, ribllatex: out,
taillatex: out,
output: out)

files
ribl: output of ri program

rilap:  parameters to control the program.

1: two integers that define the range of ribl to convert.

2: the lowest Ri value to print; lower values are given
a negative infinity symbol.

3: a sequence to put boxes around.  If there is no sequence,
then no boxes will be used.

4: number of decimal places for Ri values.

5: capitalize: if the first character is u or c, it the sequence
and bases are uppercase.  otherwise, they are lower case.

6: if the first character is h, \hline is put before and after
the labelatex, riblatex and senulatex.

7: if the first character is b, make a box around each Ri(b,l)
value corresponding to the sequence.

8: if the first character is b, make everything boldface.

headlatex: start of table format for LaTeX

labelatex: label line format for LaTeX

sequlatex: table format for LaTeX of the sequence as letters

senulatex: table format for LaTeX of the sequence as numbers

freqlatex: table format for LaTeX of the frequencies of bases

ribllatex: table format for LaTeX of the weight matrix with the
weights for the sequence boxed.

taillatex: end of table format for LaTeX

output: messages to the user

description
Read the ribl and reformat it so it can be used in a LaTeX table.  Also
generate the sequence matrix, and box the sequence on the ribl table.  The
program also supplies a table header, a label line and a tail.  These can
be concatenated together.  The user may can insert whatever they want
between parts or do other things to the table.

examples

This UNIX command concatenates the parts together:

rila
cat \
version   \
labelatex \
sequlatex \
senulatex \
midfigure \
labelatex \
ribllatex \
taillatex \
> tabular.tex

The user creates two files, morehead and midfigure.

Here is a rilap:

-3 6     two integers that define the range of ribl to convert.
-10      the lowest Ri value to print; lower values are given
caggtctgca
1        number of decimal places for Ri values
c        u or c = upper case sequence and bases
h        h = hlines given
b        b = box the sequence on the ribl matrix
b        b = boldface everything

rilap: parameters for rila version 1.39 or higher

documentation

See Figure 1 of

@article{Schneider.Ri,
author = "T. D. Schneider",
title = "Information Content of Individual Genetic Sequences",
journal = "J. Theor. Biol.",
volume = "189",
number = "4",
pages = "427-441",
{http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}
{http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}",
year = "1997"}

program that makes the ribl file:  ri.p

http://www.lecb.ncifcrf.gov/~toms/paper/ri/

author
Thomas Dana Schneider

bugs

A bug in LaTex will not allow one to read the taillatex in without getting
extra junk on the end of the table.  You can either concatenate the parts
of the table together and read it all at once or you can supply your own
'\end{tabular}'.

technical notes

*)
(* end module describe.rila *)
{This manual page was created by makman 1.45}