Delila Program: delinst

delinst program

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

{   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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