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{ version = 1.19; (* of delinst.p 2013 Aug 26}
(* begin module describe.delinst *)
(*
name
delinst: create delila instructions from lists
synopsis
delinst(title: in,
organism: in, chromosome: in, piece: in, names: in,
coordinates: in,
coordinates2: in,
directions: in, delinstp: in,
inst: out, output: out)
files
title: Delila instructions for the title, organism, chromosome and
piece along with any other controls a user wants. The title
file is copied to the top of the inst file.
organism: a list of names, one per line, for the organisms to get.
If the file is empty the program assumes that it has been specified
in the title file.
chromosome: a list of names, one per line, for the chromosomes to get.
If the file is empty the program assumes that it has been specified
in the title file.
piece: a list of names, one per line, for the pieces to get.
If the file is empty the program assumes that it has been specified
in the title file.
names: a list of names, one per line, for the pieces to get
If the file is empty no name instructions are written.
coordinates: a list of numbers, one per line, for the pieces to get
NOTE: if the first character of a coordinate is not a digit, (it
could be '-' or '+') and there are no digits in the remainder of
the string, the entire get will be dropped.
The Delila instruction format is:
get from [coordinate] [from] to same [to] [direction];
coordinates2: as with coordinates, the second coordinate of a get
replacing the 'same'.
directions: list of directions (+ or -), one per line, for the
pieces to get. 'f' (forward) and 'r' (reverse) is also
acceptable. The positive orientation is set for '+' or 'f'.
Otherwiswe the negative orientation is assumed. No checking is
done.
inst: The title file followed by name and get instructions according
to the format:
name "[NAMES]";
get from [COO] [REVDIR][FROMRANGE]
to same [DIR][TORANGE] direction [DIR];
where
[NAMES] come from the 'names' file
[REVDIR] is generated by reversing the [DIR]
[FROMRANGE] the from-range for the instructions from the 'delinstp' file
[COO] come from the 'coordinates' file
[TORANGE] the to-range for the instructions from the 'delinstp' file
[DIR] come from the 'directions' file
The name and get instruction are written to the inst file on one
line; they are shown above on several lines for clarity.
delinstp: parameters to control the program. The file must contain the
following parameters, one per line:
parameterversion: The version number of the program. This allows the
user to be warned if an old parameter file is used.
fromrange, torange (integer, integer): the range from and to for
the Delila instructions.
maxinstructions (integer): maximum number of instructions to write.
A negative value means to write all of them.
This is useful for testing before production runs.
removeduplicates (char): If 'r' then remove duplicate Delila instructions
for organism, chromosome and piece.
multiline (char): If 'm' then put instructions on multiple lines.
twocoordinates (char): If 't' then use both the coordinates and
the coordinates2 files to get the coordinates.
If the value is not 't', then the coordinates2 file
is not looked at (and so need not exist).
description
Often one needs to generate Delila instructions from data sets.
This program automates the task.
The coordinates are read in and instructions are made corresponding
to them.
If the names file is empty or reaches the end of file, the number
of the instruction is given.
If the coordinate file is empty or reaches the end of file, '+' is
assumed.
examples
documentation
see also
Program that uses the instructions: delila.p
author
Thomas Dana Schneider
bugs
technical notes
This function is now NOT active since it interferes with Delila:
NOTE: If the string for a chromosome name begins with 'chr' and is
only 5 characters long, delinst will add a '0' after 'chr'. Thus
the name 'chr1' becomes 'chr01' and will sort correctly using the
Unix sort.
*)
(* end module describe.delinst *)
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