Delila Program: reform

reform program

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

{version = 1.21; (* of reform 1994 sep 5}

(* begin module describe.reform *)
(*
name
      reform: raw sequences reformatted

synopsis
      reform(fin: in, fout: out, input: intty, output: out)

files
      fin: the raw sequences to be reformatted.  the file must contain
         only the letters: 'a', 'c', 'g', 't', and/or 'u'.
      fout: the reformatted sequence.
      input: the user defines how to reformat the sequence:
         reformat - the sequence is only reformatted.
         invert - the order of the sequence stays the same, but the bases
            are complemented.
         complement - the order of the sequence is reversed and the bases
            are complemented.
         the user also specifies the number of bases to be printed on
         each line of fout.
      output: messages to the user.

description
      Reform allows one to type a file containing raw sequence data typed in
      whatever form is convenient, and to convert it into a form that
      the merge program can use to compare to a second typed copy.
      For example, when a sequence is to be entered from two strands,
      the sequence and its complement, one can enter both strands and then
      invert the second strand for comparison by merge.  Alternatively,
      the second strand could be entered backwards and the complement taken
      using this program.

see also
      merge.p

author
      Thomas Schneider

bugs
      The first typed line is ignored because of a problem with
      the standard input procedures on Unix.  Simply type a carriage
      return when the program starts up.

*)
(* end module describe.reform *)
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