Delila Program: reffea

reffea program

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

{version = 1.02; (* of reffea.p 1997 January 12}

(* begin module describe.exon *)
(*
name
   reffea: extract references from GenBank entries as lister features

synopsis
   reffea(reffeap: in, db: in,
       reffeatures: out output: out)

files
   reffeap: parameters to control the program, one per line:

     1:  limit region somehow? zzz would need
     to have a list of accession numbers and ranges.
     need rules about how overlaps are handled
     (include only whole or with partials)

   db: a set of GenBank entries containing references:

REFERENCE   5  (bases 38597 to 38672)

   reffeatures: Locations of references in the format for the Lister
      program:

define "J02459.ref.5" "-" "<]" "[>" 0 [length-1]
@ J02459 [start] 1 "J02459.ref.5" ""

      where [length-1] is the length of the reference, minus 1 and
      [start] is the first base of the reference.

   output: messages to the user

description

   Locate references on a lister map.

examples

documentation

see also
   lister.p, exon.p

author
   Thomas Dana Schneider

bugs

   The code was created from exon.p and can be trimmed a lot.
   The parameter file contains stuff that is unnecessary
   (it's identical to exonp at the moment)

   a required parameter: version number

   a required parameter: references to include
     (in a list that ends in 0)
     or maybe better:  reference ranges to include or exclude
    include by +, exclude by -.

   parameter:

technical notes

*)
(* end module describe.exon *)
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