Delila Program: lidel

lidel program

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

{version = 1.30; (* of lidel.p 1995 July 14}

(* begin module describe.lidel *)
(*
name
   lidel: convert coordinate list to Delila instructions

synopsis
   lidel(fin: in, lidelp: in, inst: out, output: out)

files
   fin:  An input file of coordinates.  Lines beginning with "*" are ignored by
       being copied to the inst as comments.  Two columns are required:  the
       piece name and the coordinate.

   lidelp:  parameters to control the program.
      first line: 2 integers, range to use.
      second line: piecol: column number of piece name
      third line: datacol: column number of coordinate data
      fourth line: title of book
      fifth line: organism name
      sixth line: chromosome name
      seventh line: symmetry of instructions.

  If the first character on the line is 'e' then even symmetry is used
  and the center of the symmetry will lie between bases 0 and 1.

     If the first character is 'e' then there are two possible ways that
     the numbers in fin could be defined:

        If the second character on the line is 'l' then the number in
        fin is to the left (5') of the symmetry center.

        If the second character on the line is 'r' then the number in
        fin is to the right (3') of the symmetry center.

  If the first character on the line is 'o' then odd symmetry is used
  and the center of the symmetry will lie at base 0.

      eighth line: number of instructions per integer in fin.
         1: only one instruction is written.
         2: two instructions are written: same as 1 and the complement
            at the point of symmetry.

   inst:  Delila instructions which correspond to the locations in fin.

   output: messages to the user

description

   Frequently one has a list of coordinates that need to be converted
   to Delila instructions.

examples

   An example lidelp file:

-700 700   fromrange torange
1          column number of piece name
3          column number of coordinate data
CDS
Sacc.cerevisiae
Sacc.cerevisiae
er         symmetry (e)ven or (o)dd, (l)eft or (r)ight
2          number of instructions to write to fin

parameters for lidel.p

documentation

see also

author
   Thomas Dana Schneider

bugs

   The coordinates given are for a location (0) and the complement (at 1)
this assumes that the point of symmetry is at 0.5; this must be generalized.

technical notes

*)
(* end module describe.lidel *)
{This manual page was created by makman 1.44}
{created by htmlink 1.55}
U.S. Department of Health and Human Services  |  National Institutes of Health  |  National Cancer Institute  |  USA.gov  | 
Policies  |  Viewing Files  |  Accessibility  |  FOIA