Delila Program: frag

frag program

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

{version = 1.03; (* of frag.p 1999 August 25}

(* begin module describe.frag *)
(*
name
   frag: create delila instructions to grab fragments from a book

synopsis
   frag(book: in, fragp: in, fraginst: out, output: out)

files
   book:  a Delila system book, usually a whole genome

   fragp:  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): from-to range of the delila instructions

      number (integer): number of instructions to create.

      moreskip (integer): additional space between fragments.  The basic
         spacing between fragments is the length of the fragments,
         torange - fromrange + 1.  Setting moreskip to zero makes the
         fragments be next to each other.  Increasing moreskip increases
         the gap between the fragments.  Note that fragments will overlap
         if moreskip is less than zero.

   fraginst:  delila instructions for grabbing fragments, according to fragp

   fragfeatures:  lister features corresponding to the instructions.

   output: messages to the user

description

   Frag allows one to obtain non-overlapping fragments of a genome
   for multiple alignment by malign.

examples

fragp:

1.00  version of frag that this parameter file is designed for.
-400 +400  fromrange, torange: From-to range of instructions
100        number: number of instructions to make
  0        moreskip: additional space between fragments

documentation

see also
   delila.p, malign.p, lister.p

author
   Thomas Dana Schneider

bugs

technical notes

*)
(* end module describe.frag *)
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