Delila Program: parse

parse program

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

{   version = 2.31; (* of parse.p 2017 Aug 14}

(* begin module describe.parse *)
(*
name
      parse: breaks a book into its components

synopsis
      parse(book: in, list: out, parsep: in, output: out)

files
      book: a book from the delila system
      list: a listing of the parts in the book
      parsep: parse parameters from the user
         If parsep is empty, default values are used.  Otherwise, parsep
         must contain four lines corresponding to the variables
         that the user may reset.  They are:
            number of bases printed per line
            symbol to mark the end of sequences
            print header information
            print information about each sequence
            print raw sequences
         the last 3 items are boolean (true/false) values.  If you want to
         have the information, put a t (standing for true) at the beginning of
         the line.  If you do not want it, put an f (standing for false).

         Creating FastA format:

         If the 'symbol to mark the end of sequences' is 'f' then no
         symbol will be at the end and fasta format will be generated.
         This is just a '>' followed by information about the piece
         and then the corresponding sequence.

         Note: dnacurve.py from
         http://www.lfd.uci.edu/~gohlke/code/dnacurve.py.html
         uses fasta format but if there is a space after the '>'
         it will crash.

      output: messages to the user

description
      To parse is to break into component parts.  This program breaks a book
      into parts.  This allows one to easily look at sequences of a book
      without having to look at the book structure or the fancy listing
      provided by the lister program.

examples
      if parsep contains 60/./f/f/t then the sequences will be listed, with
      the '.' character ending each sequence.  all other information would be
      lost.

author
     Thomas Schneider

bugs
      Only piece information is listed.

*)
(* end module describe.parse *)
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