{version = 1.16; (* of winrs.p 1996 April 10}
(* begin module describe.winrs *)
(*
name
winrs: Compute Rs/window vs window in a single program
synopsis
winrs(book: in, cmp: in, winrsp: in, xyin: out, output: out)
files
book: A book from Delila. Only the first DNA piece in the book is used.
cmp: A composition from the comp program.
If cmp is empty, then equal frequencies are assumed.
winrsp: : Parameters to control the program: one per line
StartCoordinate (integer): The base of the sequence to be used for the
zero coordinate of the first window. For simplicity, internal
coordinates are used: the sequence begins at base 1.
MinimumWindowSize (integer): The shortest window to use for the
computations.
MaximumWindowSize (integer): The longest window to use for the
computations.
SpaceBetweenWindows (integer): Windows are spaced so as to not
collide. You can add extra distance with this parameter.
If it is negative, the windows will overlap.
NumberofWindows (integer): The number of windows to use for
each computation.
* The program will object if any of these parameters cause a window to
go outside the sequence.
xyin: output of this program, input to the xyplo graphics program.
columns:
1: window size
2: Rs, Rsequence, bits
3: SD, Standard Deviation of Rs, bits
4: Rs/(window size), bits/base
5: SD/(window size), bits/base
output: messages to the user
description
A window size is chosen. The first sequence in the book is broken into
fragments of this size. These are aligned and the information content,
Rsequence (Rs) is computed. This process is repeated for a range of
window sizes defined in the parameters. The output is a data file (xyin)
containing columns for window size (w), Rs and the standard deviation of
Rs (SD). There are also two normalized columns for Rs/w and SD/w, which
are reports in bits per base. Repeating structures will appear as peaks
in a graph of Rs/w versus w.
examples
documentation
[1996 April 8]
see also
lidel.p, winscan.p, delila.p, encode.p, rseq.p, xyplo.p
author
Thomas Dana Schneider
bugs
The program should produce a xyplop so that it can put
the genomic information on the curve automatically.
technical notes
Paremeter dnamax must be set as large as possible so that the entire
sequence can fit into a single array and therefore be accessed as rapidly
as possible. Since Delila stores sequences with 2 bits/base (assuming a
good compiler) so one can compute the size of the array in bytes.
*)
(* end module describe.winrs *)
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