Delila Program: rila

rila program

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   \
headlatex \
    morehead  \
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",
note = "\htmladdnormallink
{http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}
{http://www.lecb.ncifcrf.gov/\~{}toms/paper/ri/}",
year = "1997"}

see also

   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 *)
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