#!/bin/csh -f #(ie run the cshell on this but don't read the .cshrc) # version = 1.01 of run.ev 2000Jul18.01:00:47 # origin 2000Jul18.01:00:47 # This csh script will run the evolution program # and then display the results in PostScript in the logo file. # You can rerun it to step through an evolution. # For complete documentation see: # http://www.lecb.ncifcrf.gov/~toms/delila/evd.html # The first parts of the script simply create the input files # you need to run the Delila programs. # The programs are all run at the end. # **************************************************************************** if (-f evp) then echo using previous evp file else echo "creating an evp file for you" cat <<__EOD__>evp 3.42 version of ev that this parameter file is designed for. 16 NUMBER OF CREATURES 128 NUMBER OF BASES PER CREATURE, G 8 NUMBER OF SITES PER CREATURE, gamma 5 WIDTH OF THE RECOGNIZER IN BASES 4 BASES PER INTEGER OF THE RECOGNIZER 1 MUTATION RATE IN HITS PER CREATURE PER GENERATION 0.30 SEED FOR THE RANDOM NUMBER GENERATOR 10 CYCLES 1 DISPLAY INTERVAL 1c3gr4s a=av, c=change, i=indivls, g=Hg, r=Rs, o=orbit, s=status true SELECTING 1000 STORAGE FREQUENCY a r = random site placement, n = no overlap random, a = array 0 sigma __EOD__ endif if (-f all) then echo using previous all file else echo "creating an all file for you" touch all endif # **************************************************************************** if (-f evdp) then echo using previous evdp file else echo "creating an evdp file for you" cat <<__EOD__>evdp 2.26 version of evd that this parameter file is designed for. 1 firstcreature: the number of the first creature to display 1 secondcreature: the number of the last creature to display non-site features: if the first character is 'n' then show non-sites __EOD__ endif # **************************************************************************** if (-f makebkp) then echo using previous makebkp file else echo "creating a makebkp file for you" cat <<__EOD__>makebkp a evolving binding sites __EOD__ endif # **************************************************************************** if (-f inst) then echo using previous inst file else echo "creating an inst file for you" touch inst endif if (-f encodep) then echo using previous encodep file else echo "creating an encodep file for you" cat <<__EOD__>encodep f f: first base, i: inst, b: book alignment -100 100 1 1 1 1 __EOD__ endif # **************************************************************************** if (-f cmp) then echo using previous cmp file else echo "creating a cmp file for you" touch cmp endif # **************************************************************************** if (-f dalvecp) then echo using previous dalvecp file else echo "creating a dalvecp file for you" touch dalvecp endif # **************************************************************************** if (-f makelogop) then echo using previous makelogop file else echo "creating a makelogop file for you" cat <<__EOD__>makelogop 0 +20 FROM to TO range to make the logo over 100 sequence coordinate before which to put a bar on the logo 5.0 10.0 (xcorner, ycorner) lower left hand corner of the logo (in cm) 0 rotation: angle to rotate the graph 0.36 charwidth: (real, > 0) the width of the logo characters, in cm 5 0.1 barheight, barwidth: (real, > 0) height of vertical bar, in cm 2 barbits: (real) height of the vertical bar, in bits; < 0: no I-beam bars no barends: if 'b' put bars before and after each line no show showingbox: if 's' show a box around each character, 'f' = fill no outline outline: if 'o' make each character as an outline caps no caps: if 'c', alphabetic characters are converted to caps 41 stacksperline: number of character stacks per line output 1 linesperpage: number of lines per page output 1.0 linemove: line separation relative to the barheight numbers - numbering: if the first letter is 'n' then each stack is numbered 1 shrinking: factor by which to shrink characters inside dashed box 1 strings: the number of user defined strings to follow -1000 5.2 1 coordinates (in cm) and scale of the first string \n 0 evolution binding sites n 2 1 2 1 edgecontrol (p=page), edgeleft, edgeright, edgelow, edgehigh in cm d d: 5' 3'; p: N C; else: nothing shown on ends makelogop: parameters for the makelogo program, version 8.76 or higher __EOD__ endif if (-f colors) then echo using previous colors file else echo "creating a colors file for you" cat <<__EOD__>colors * Color scheme for logos of DNA (for the makelogo program). * color order is red-green-blue * * green: * A 0 1 0 * a 0 1 0 * This makes the green slightly less dark on the Tektronix Phaser 140: A 0.182082 1 0.181899 a 0.182082 1 0.181899 * * blue: * This combination of red, green and blue makes a pretty egg shell blue color * on the Tektronix colorquick printer after processing by Freedom of the Press * to convert from PostScript 1991 January 16 C 0 0.9372 1 c 0 0.9372 1 * * red: T 1 0 0 t 1 0 0 U 1 0 0 u 1 0 0 * * orange: G 1 0.7 0 g 1 0.7 0 __EOD__ endif if (-f marks) then echo using previous marks file else echo "creating a marks file for you" touch marks endif if (-f wave) then echo using previous wave file else echo "creating a wave file for you" touch wave endif # **************************************************************************** # run the Delila programs ev # evolve the creatures with ev.p evd # make the display files with this program, evd.p cp sites sequ # copy the sites file to the sequ file (a unix command) makebk < makebkp # make the delila book with makebkp and makebk.p encode # be sure to use the f mode in encodep with encode.p rseq # compute information using the rseq.p program dalvec # make the symvec using the dalvec.p program makelogo # make the logo from the symvec with makelogo.p. echo "" echo The PostScript sequence logo is in the logo file.