vq/make_residue_books.pl

   1 #!/usr/bin/perl
   2
   3 # quick, very dirty little script so that we can put all the
   4 # information for building a residue book set (except the original
   5 # partitioning) in one spec file.
   6
   7 #eg:
   8
   9 # >res0_128_128 interleaved
  10 # haux res0_96_128aux.vqd 0,4,2
  11 # :1 res0_128_128_1.vqd, 4, nonseq cull, 0 +- 1
  12 # +1a, 4, nonseq, 0 +- .25 .5
  13 # :2 res0_128_128_2.vqd, 4, nonseq, 0 +- 1 2
  14 # :3 res0_128_128_3.vqd, 4, nonseq, 0 +- 1 3 5
  15 # :4 res0_128_128_4.vqd, 2, nonseq, 0 +- 1 3 5 8 11
  16 # :5 res0_128_128_5.vqd, 1, nonseq, 0 +- 1 3 5 8 11 14 17 20 24 28 31 35 39
  17 # +1a, 4, nonseq, 0 +- .5 1
  18
  19
  20 die "Could not open $ARGV[0]: $!" unless open (F,$ARGV[0]);
  21
  22 $goflag=0;
  23 while($line=<F>){
  24
  25     print "\n#### $line\n\n";
  26     if($line=~m/^GO/){
  27         $goflag=1;
  28         next;
  29     }
  30
  31     if($goflag==0){
  32         if($line=~m/\S+/ && !($line=~m/^\#/) ){
  33             my $command=$line;
  34             print ">>> $command\n";
  35             die "Couldn't shell command.\n\tcommand:$command\n"
  36                 if syst($command);
  37         }
  38         next;
  39     }
  40
  41     # >res0_128_128
  42     if($line=~m/^>(\S+)\s+(\S*)/){
  43         # set the output name
  44         $globalname=$1;
  45         $interleave=$2;
  46         next;
  47     }
  48
  49     # haux res0_96_128aux.vqd 0,4,2
  50     if($line=~m/^h(.*)/){
  51         # build a huffman book (no mapping)
  52         my($name,$datafile,$arg)=split(' ',$1);
  53         my $command="huffbuild $datafile $arg > $globalname$name.vqh";
  54         print ">>> $command\n";
  55         die "Couldn't build huffbook.\n\tcommand:$command\n"
  56             if syst($command);
  57         next;
  58     }
  59
  60     # :1 res0_128_128_1.vqd, 4, nonseq, 0 +- 1
  61     if($line=~m/^:(.*)/){
  62         my($namedata,$dim,$seqp,$vals)=split(',',$1);
  63         my($name,$datafile)=split(' ',$namedata);
  64         # build value list
  65         my$plusminus="+";
  66         my$list;
  67         my$count=0;
  68         foreach my$val (split(' ',$vals)){
  69             if($val=~/\-?\+?\d+/){
  70                 if($plusminus=~/-/){
  71                     $list.="-$val ";
  72                     $count++;
  73                 }
  74                 if($plusminus=~/\+/){
  75                     $list.="$val ";
  76                     $count++;
  77                 }
  78             }else{
  79                 $plusminus=$val;
  80             }
  81         }
  82         die "Couldn't open temp file temp$$.vql: $!" unless
  83             open(G,">temp$$.vql");
  84         print G "$count $dim 0 ";
  85         if($seqp=~/non/){
  86             print G "0\n$list\n";
  87         }else{
  88             print G "1\n$list\n";
  89         }
  90         close(G);
  91
  92         my $command="latticebuild temp$$.vql > $globalname$name.vqh";
  93         print ">>> $command\n";
  94         die "Couldn't build latticebook.\n\tcommand:$command\n"
  95             if syst($command);
  96
  97         my $command="latticehint $globalname$name.vqh > temp$$.vqh";
  98         print ">>> $command\n";
  99         die "Couldn't pre-hint latticebook.\n\tcommand:$command\n"
 100             if syst($command);
 101
 102         if($interleave=~/non/){
 103             $restune="res1tune";
 104         }else{
 105             $restune="res0tune";
 106         }
 107
 108         if($seqp=~/cull/){
 109             my $command="$restune temp$$.vqh $datafile 1 > $globalname$name.vqh";
 110             print ">>> $command\n";
 111             die "Couldn't tune latticebook.\n\tcommand:$command\n"
 112                 if syst($command);
 113         }else{
 114             my $command="$restune temp$$.vqh $datafile > $globalname$name.vqh";
 115             print ">>> $command\n";
 116             die "Couldn't tune latticebook.\n\tcommand:$command\n"
 117                 if syst($command);
 118         }
 119
 120         my $command="latticehint $globalname$name.vqh > temp$$.vqh";
 121         print ">>> $command\n";
 122         die "Couldn't post-hint latticebook.\n\tcommand:$command\n"
 123             if syst($command);
 124
 125         my $command="mv temp$$.vqh $globalname$name.vqh";
 126         print ">>> $command\n";
 127         die "Couldn't rename latticebook.\n\tcommand:$command\n"
 128             if syst($command);
 129
 130         # run the training data through book to cascade
 131         if($interleave=~/non/){
 132             $vqcascade="vqcascade";
 133         }else{
 134             $vqcascade="vqcascade -i";
 135         }
 136
 137         my $command="$vqcascade +$globalname$name.vqh $datafile > temp$$.vqd";
 138         print ">>> $command\n";
 139         die "Couldn't cascade latticebook.\n\tcommand:$command\n"
 140             if syst($command);
 141
 142
 143         my $command="rm temp$$.vql";
 144         print ">>> $command\n";
 145         die "Couldn't remove temp files.\n\tcommand:$command\n"
 146             if syst($command);
 147
 148         next;
 149     }
 150     # +a 4, nonseq, 0 +- 1
 151     if($line=~m/^\+(.*)/){
 152         my($name,$dim,$seqp,$vals)=split(',',$1);
 153
 154         # build value list
 155         my$plusminus="+";
 156         my$list;
 157         my$count=0;
 158         foreach my$val (split(' ',$vals)){
 159             if($val=~/\-?\+?\d+/){
 160                 if($plusminus=~/-/){
 161                     $list.="-$val ";
 162                     $count++;
 163                 }
 164                 if($plusminus=~/\+/){
 165                     $list.="$val ";
 166                     $count++;
 167                 }
 168             }else{
 169                 $plusminus=$val;
 170             }
 171         }
 172         die "Couldn't open temp file temp$$.vql: $!" unless
 173             open(G,">temp$$.vql");
 174         print G "$count $dim 0 ";
 175         if($seqp=~/non/){
 176             print G "0\n$list\n";
 177         }else{
 178             print G "1\n$list\n";
 179         }
 180         close(G);
 181
 182         my $command="latticebuild temp$$.vql > $globalname$name.vqh";
 183         print ">>> $command\n";
 184         die "Couldn't build latticebook.\n\tcommand:$command\n"
 185             if syst($command);
 186
 187         my $command="latticehint $globalname$name.vqh > temp$$.vqh";
 188         print ">>> $command\n";
 189         die "Couldn't pre-hint latticebook.\n\tcommand:$command\n"
 190             if syst($command);
 191
 192         if($interleave=~/non/){
 193             $restune="res1tune";
 194         }else{
 195             $restune="res0tune";
 196         }
 197
 198         if($seqp=~/cull/){
 199             my $command="$restune temp$$.vqh temp$$.vqd 1 > $globalname$name.vqh";
 200             print ">>> $command\n";
 201             die "Couldn't tune latticebook.\n\tcommand:$command\n"
 202                 if syst($command);
 203         }else{
 204             my $command="$restune temp$$.vqh temp$$.vqd > $globalname$name.vqh";
 205             print ">>> $command\n";
 206             die "Couldn't tune latticebook.\n\tcommand:$command\n"
 207                 if syst($command);
 208         }
 209
 210         my $command="latticehint $globalname$name.vqh > temp$$.vqh";
 211         print ">>> $command\n";
 212         die "Couldn't post-hint latticebook.\n\tcommand:$command\n"
 213             if syst($command);
 214
 215         my $command="mv temp$$.vqh $globalname$name.vqh";
 216         print ">>> $command\n";
 217         die "Couldn't rename latticebook.\n\tcommand:$command\n"
 218             if syst($command);
 219
 220         # run the training data through book to cascade
 221         if($interleave=~/non/){
 222             $vqcascade="vqcascade";
 223         }else{
 224             $vqcascade="vqcascade -i";
 225         }
 226
 227         my $command="$vqcascade +$globalname$name.vqh temp$$.vqd > tempa$$.vqd";
 228         print ">>> $command\n";
 229         die "Couldn't cascade latticebook.\n\tcommand:$command\n"
 230             if syst($command);
 231
 232
 233         my $command="rm temp$$.vql";
 234         print ">>> $command\n";
 235         die "Couldn't remove temp files.\n\tcommand:$command\n"
 236             if syst($command);
 237
 238         my $command="mv tempa$$.vqd temp$$.vqd";
 239         print ">>> $command\n";
 240         die "Couldn't rename temp file.\n\tcommand:$command\n"
 241             if syst($command);
 242
 243         next;
 244     }
 245 }
 246
 247 $command="rm temp$$.vqd";
 248 print ">>> $command\n";
 249 die "Couldn't remove temp files.\n\tcommand:$command\n"
 250     if syst($command);
 251
 252 sub syst{
 253     system(@_)/256;
 254 }