Delila Program: rawbk

rawbk program

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

{  version = 3.22; (* of rawbk.p 2004 Mar 8}

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

      rawbk(raw: in, rawchanges: out, book: out, input: intty, output: out)

      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.
         A,C,G,T, and U, are also accepted now.

      rawchanges:  Delila programs cannot handle sequences that have
  ambiguities because Delila was designed on the assumption that
  people would finish their sequences.  Unfortunately this is not
  true, and the databases contain bases other than acgt to indicate
  ambiguity.  These are converted to "a" and the cases are reported in
  this file.  NOTE:  "u" is converted to "t".

      book: a file which contains the sequence in the book form
         such that it will interface with the delila system programs.

      input: the interactive input from the keyboard. rawbk needs to
         get some information from the user to name the sequence.

      output: where error messages will appear.

      The purpose of this program is to allow one to rapidly create a book
      from a raw sequence. rawbk 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.
      It will flag any letters other than 'a','c','g','t', or 'u', that appear
      in the file and note their locations. it will count the bases. if any
      characters were flagged, or any other error occurs, rawbk will
      put 'halt' into the book, in the same form the librarian does, to
      prevent further use of the book.  Otherwise, the book is constructed
      to contain one piece of sequence.  The coordinates begin with base 1.

see also
      dbbk.p, makebk.p, lister.p

      Thomas D. Schneider

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

(* end module describe.rawbk *)
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