Delila Program: rwbk

rwbk program

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

{version = 1.15; (* of rwbk.p 2000 Feb 18}

(* begin module describe.rwbk *)
(*
name
      rwbk: make a raw sequence into a book

synopsis
      rwbk(raw: in, book: out, output: out)

files
      raw: a file with a sequence on it, that is only the letters
         a,c,g,t, or u, with any spacing and carriage returns.
      book: a file which contains the sequence in the book form
         such that it will interface with the delila system programs.
      output: where error messages will appear.

description
      The purpose of this program is to allow one to rapidly create a book
      from a raw sequence. rwbk will take a 'raw' sequence and put it into
      the standard form of a book so that the delila system programs can be
      used on the sequence.  The user is asked for one name, which will
      become the name of all things in the book (title, organism,
      chromosome and piece).
         The program reads thru 'raw', keeping track of characters and lines.
      unlike rawbk, it accepts bases:
         'a','c','m','g','r','s','v','t',
         'w','y','h','k','d','b','n'
      but converts them to the first matching base of acgt.

      The book is constructed to contain one piece of sequence.  The
      coordinates begin with base 1.

see also
      makebk.p

author
      Thomas D. Schneider

bugs
      The program should use book writing routines from delmods, but it
      has not been updated yet.

*)
(* end module describe.rwbk *)
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