Delila Program: modin

modin program

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

{version = 1.44; (* of modin.p 1994 sep 5}

(* begin module describe.modin *)
(*
name
      modin: generate modularized delila instructions for absolute sites

synopsis
      modin(fin: in, inst: out, output: out)

files
      fin: sequence site positions in a special format.
      inst:  modularized delila instructions
      output: messages to the user

description
      The existence of a file containing modularized delila instructions
      allows one to pull, from the file, instructions for generating
      specific sequence sites using the module program.  For instance,
      using modin, one may make a file containing delila instructions for
      all the laci amber mutation sites, one site per module.  Then, using
      the module program, one could pull from the file instructions for
      sites a9, a16, a19, and a21 by using the module program.  This
      would be useful if one had several different sets of amber mutations
      to analyse separately.

see also
      module.p, delila.p, describe.modin.use

author
      John Hoffhines

bugs
      The program has not been used much, so its usefulness is not known.

*)
(* end module describe.modin *)
{version = 1.43; of describe.modin.use 1993 Jan 27 *)}

(* begin module describe.modin.use *)
(*
name
      modin.use: more information on using the modin program

     MODIN FIN FILE FORMAT (BNF)

<BOOK TITLE><SETS>
<SETS>::=<SET>|<SET><SETS>
<SET>::=SET <KEY> <KEY> <KEY> <KEY> <SIGNED NUMBER> <SIGNED NUMBER>
            <MODULE GROUP>
<MODULE GROUP>::=<MODULE PARAMETERS>|<MODULE GROUP> <MODULE PARAMETERS>
<MODULE PARAMETERS>::=M <NUMBER> <IDENTIFIER>|<NUMBER> <IDENTIFIER>

     NOTES ON MODIN FIN FILE FORMAT

1) Any terms undefined here are defined in LIBDEF.

2) Keys designate, respectively, the words "organism", "chromosome",
    and "p" (piece), "g" (gene), or "t" (transcript).

3) The module parameter "m" sets delila instructions direction
    to - for one module only.  Default is +.

4) Within the module parameters section, "number" is DNA base position,
   and "identifier" immediately following it is that which will be
   used in that position's module name.

5) Only one set per line is allowed, without its module group.  Module
   groups follow on subsequent lines; more than one per line is allowed,
   but they may not be truncated by the end of a line.

*)
(* end module describe.modin.use *)
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