Delila Program: coda

coda program

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

{version = 2.05; (* of coda, 1994 Sep 5}

(* begin module describe.coda *)
(*
name
      coda: composition file to data for genhis

synopsis
      coda(cmp: in, data: out, codap: in, output: out)

files
      cmp: a composition, the output of program comp
      data: identification lines are followed by
         the number of occurences of each oligo and the sequence
         of the oligo, one pair per line.  the form of the
         file can be changed using the parameters in codap.
      codap: parameter file.  four parameters, one per line.
         1. composition depth to be used in the data file (integer)
         2. the least frequent oligo to record in data (integer).
         3. the most frequent oligo to record in data (integer).
         4. if the first character is 'b', the number of each
         oligo is given before the oligo, 'a' means after.
         'n' means do not give the number.  's' means the data file will be
         used as input to the search program.  no numbers are given and
         commands to search are made which will result in a list
         of the locations of the selected oligos.
            if parameters 2 to 4 are missing they default to
            0 100000 b.

      output: messages to the user

description
      coda converts a composition file from the comp program
      into a list of oligos.  unlike the original composition
      file, this list may contain all oligos of the length desired
      (to save space, comp removes an n-long oligo when the
      two n-1 long oligos inside it do not exist).  however,  coda
      can be told to only include frequent or infrequent oligos
      using the parameter file.  two ways to use the data are:
      1. use the data file as input to genhis to determine the
      distribution of the composition.
      2. use the 's' feature to generate instructions for the
      search program.  search converts the list of oligos to
      locations in a sequence.  unshi then is used to remove
      the extra blanks and genhis then gives a map of the
      locations of rare or common oligos.

example
      file: datat7

see also
      comp.p, genhis.p, search.p, unshi.p

author
      thomas dana schneider

bugs
      none known
*)
(* end module describe.coda *)
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