bin/scm

   1 #!/usr/local/bin/perl
   2
   3 use FindBin qw($Bin);
   4 use lib "$Bin/../lib";
   5
   6 # Don't edit the line below, it must look exactly like this.
   7 # Everything above this line will be replaced #
   8
   9 use PsN;
  10 use file;
  11 use model;
  12 use tool::scm;
  13 use tool::scm::config_file;
  14 use debug;
  15 use strict;
  16 use Getopt::Long;
  17 use Cwd;
  18 use common_options;
  19 use ui;
  20
  21 my $cmd_line = $0 . " " . join( " ", @ARGV );
  22
  23 my %options;
  24
  25 my %required_options = ( "config_file:s" => '');
  26
  27 my %optional_options = ( "fix" => '',
  28                          "search_direction:s" => 'forward|backward|both',
  29                          "gof:s" => '',
  30                          "global_init:s" => '',
  31                          "logfile:s" => '',
  32                          "model:s" => '',
  33                          "backwards_dir:s" => '',
  34                          "p_value:s" => '',
  35                          "p_forward:s" => '',
  36                          "p_backward:s" => '',
  37                          "do_not_drop:s" => '');
  38
  39 my $res = GetOptions( \%options,
  40                       @common_options::get_opt_strings,
  41                       keys(%required_options),
  42                       keys(%optional_options)
  43                       );
  44 exit unless $res;
  45
  46 common_options::set_globals( \%options );
  47
  48 my %help_text;
  49 $help_text{Pre_help_message} = <<'EOF';
  50   <h3 class="heading1">scm</h3>
  51
  52   Perl script for stepwise covariate model building from NONMEM models.
  53
  54   <h3 class="heading1">Usage:</h3>
  55 EOF
  56
  57     $help_text{Description} = <<'EOF';
  58   <h3 class="heading1">Description:</h3>
  59
  60     The Stepwise Covariate Model (SCM) building tool of PsN implements
  61     Forward Selection and Backward Elimination of covariates to a
  62     model. In short, one model for each relevant parameter-covariate
  63     relationship is prepared and tested in a univariate manner. In the
  64     first step the model that gives the best fit of the data according
  65     to some criteria is retained and taken forward to the next
  66     step. In the following steps all remaining parameter-covariate
  67     combinations are tested until no more covariates meet the criteria
  68     for being included into the model. The Forward Selection can be
  69     followed by Backward Elimination, which proceeds as the Forward
  70     Selection but reversely, using stricter criteria for model
  71     improvement.
  72     <br><br>
  73     The Stepwise Covariate Model building procedure is run by the scm
  74     utility. The options to the scm utility are of three diffrent
  75     types, first are the common options which works like the common
  76     options for all tools. Then are the SCM specific command line
  77     options. And last are options which have a more complex structures
  78     and are considered to cumbersome to specify on the command
  79     line. These options must therefore be specified in a separate
  80     configuration file. It is possible to provide values for all
  81     options, including the common options, in the configuration file
  82     but it should be noted that the command line overrides the
  83     configuration file, if an option is specified at both
  84     locations.
  85
  86     <!--/>Read more on our homepage: www.sf.net/psn.<-->
  87
  88 EOF
  89
  90     $help_text{Examples} = <<'EOF';
  91   <h3 class="heading1">Examples:</h3>
  92
  93     Execute an SCM using parameters set in the config file
  94     'phenobarbital.scm'.
  95
  96        <p class="style2">$ scm -config_file=phenobarbital.scm</p>
  97
  98     Execute an SCM using parameters set in the config file
  99     'phenobarbital.scm'. But override the retries and the seed
 100     parameter.
 101
 102        <p class="style2">$ scm -config_file=phenobarbital.scm -retries=5 -seed=12345 phenobarbital.mod</p>
 103 EOF
 104
 105     $help_text{Options} = <<'EOF';
 106   <h3 class="heading1">Options:</h3>
 107
 108     The options are given here in their long form. Any option may be
 109     abbreviated to any nonconflicting prefix. The -threads option may
 110     be abbreviated to <span class="style2">-thr</span> but <span class="style2">-debug</span> may not be abbreviated to <span class="style2">-d</span>
 111     because it conflicts with <span class="style2">-debug_packages</span> and <span class="style2">-debug_subroutines</span>.
 112
 113     The following options are valid:
 114 EOF
 115
 116     $help_text{-h} = <<'EOF';
 117     <p class="style2">-h | -?</p>
 118
 119     With -h or -? scm will print a list of options and exit.
 120 EOF
 121
 122     $help_text{-help} = <<'EOF';
 123     <p class="style2">-help</p>
 124
 125     With -help scm will print this, longer, help message.
 126 EOF
 127
 128     $help_text{-config_file} = <<'EOF';
 129     <p class="style2">-config_file</p>
 130
 131     A path and file name to an scm configuration file.
 132 EOF
 133
 134     $help_text{-fix} = <<'EOF';
 135     <p class="style2">-fix</p>
 136 EOF
 137
 138     $help_text{-search_direction} = <<'EOF';
 139     <p class="style2">-search_direction</p>
 140
 141     Which search task to perform: backward, forward or both is allowed.
 142 EOF
 143
 144     $help_text{-gof} = << 'EOF';
 145     <p class="style2">-gof</p>
 146 EOF
 147
 148     $help_text{-global_init} = << 'EOF';
 149     <p class="style2">-global_init</p>
 150 EOF
 151
 152     $help_text{-logfile} = << 'EOF';
 153     <p class="style2">-logfile</p>
 154
 155     The name of the logfile.
 156 EOF
 157
 158     $help_text{-model} = << 'EOF';
 159     <p class="style2">-model</p>
 160
 161     The name of the basic model file, without any parameter-covariate
 162     relations included.
 163 EOF
 164
 165     $help_text{-p_value} = << 'EOF';
 166     <p class="style2">-p_value</p>
 167
 168     Use this option to set the p_value for both forward and backward
 169     steps.
 170 EOF
 171
 172     $help_text{-p_forward} = << 'EOF';
 173     <p class="style2">-p_forward</p>
 174
 175     Using the p_forward option, you can specify the p-value to use for
 176     the forward selection.
 177 EOF
 178
 179     $help_text{-p_backward} = << 'EOF';
 180     <p class="style2">-p_backward</p>
 181
 182     Using the p_backward option, you can specify the p-value to use
 183     for the backward deletion.
 184 EOF
 185
 186     $help_text{-do_not_drop} = << 'EOF';
 187     <p class="style2">-do_not_drop</p>
 188
 189     Since the number of columns are restricted to 20 for NONMEM it is
 190     necessary to minimize the number of undropped columns. The scm
 191     utility uses the '=DROP' syntax of NONMEM to exclude the covariate
 192     columns that are not used. If some covariates are used in the PK
 193     or PRED code in the basic model you must list them using the
 194     do_not_drop option to prevent them from being dropped.
 195 EOF
 196
 197     $help_text{Post_help_message} = <<'EOF';
 198     Also see 'execute.pl -help' for a description of common options.
 199 EOF
 200
 201 common_options::online_help( 'scm', \%options, \%help_text, \%required_options, \%optional_options);
 202
 203 if ( $options{'config_file'} eq '' ){
 204   print "Please specify a config file \n";
 205   exit;
 206 }
 207
 208 'ui' -> category( 'scm' );
 209 'ui' -> silent(1) if( $options{'silent'} );
 210
 211 debug -> level( $options{'debug'} );
 212 debug -> package( $options{'debug_package'} );
 213 debug -> subroutine( $options{'debug_subroutine'} );
 214 debug -> warn_with_trace( $options{'warn_with_trace'} );
 215
 216 my $config_file;
 217 if( -e $options{'config_file'} ){
 218   my $file = file -> new( name => $options{'config_file'}, path => '.' );
 219   $config_file = 'tool::scm::config_file' -> new ( file => $file );
 220
 221   foreach my $option ( keys %{$config_file -> valid_scalar_options} ){
 222     if( $options{$option} ) {
 223       $config_file -> $option($options{$option});
 224     }
 225   }
 226
 227   foreach my $option ( keys %{$config_file -> valid_code_options} ){
 228     if( $options{$option} ){
 229       $config_file -> $option(eval($options{$option}));
 230     }
 231   }
 232
 233   foreach my $option ( keys %{$config_file -> valid_array_options} ){
 234     if( $options{$option} ){
 235       my @arr = split( /,/ , $options{$option});
 236       $config_file -> $option(\@arr);
 237     }
 238   }
 239
 240 } else {
 241   print "Error: config file $options{'config_file'} is missing.\n" ;
 242   exit;
 243 }
 244
 245 # Moved here as a quick fix. Consider automating option handling from
 246 # the config file diagram.
 247 common_options::get_defaults( \%options, 'scm' );
 248
 249 my $eval_string = common_options::model_parameters(\%options);
 250
 251 if( defined $config_file and $config_file -> extra_data_files ){
 252   foreach my $extra_data_file ( keys %{$config_file -> extra_data_files} ){
 253     push( @{$options{'extra_data_files'}}, $extra_data_file );
 254     push( @{$options{'extra_data_headers'}}, $config_file -> extra_data_files -> {$extra_data_file} );
 255   }
 256 }
 257
 258 if( defined $config_file -> gof ) {
 259   use lib getcwd();
 260   my $tmp = $config_file -> gof;
 261   require $tmp.".pm";
 262 #  $tmp =~ s/\.pm//;
 263   $tmp = $tmp.'::test';
 264   $config_file -> gof( \&$tmp );
 265 }
 266
 267 my $models_array = [ model -> new ( eval $eval_string,
 268                                     filename           => $config_file -> model,
 269                                     target             => 'disk' ) ] ;
 270
 271 my $direction = $config_file -> search_direction;
 272
 273 my $scm;
 274
 275 if( $direction eq 'forward' or $direction eq 'both' ){
 276   print ui -> print( category => 'scm',
 277                      message => "Starting scm forward search" );
 278
 279   my $orig_ofv;
 280   my $orig_p_value;
 281   if( -e $options{'config_file'} ){
 282
 283     if( defined $config_file -> ofv_forward ){
 284       $orig_ofv = $config_file -> ofv_change;
 285       $config_file -> ofv_change($config_file -> ofv_forward);
 286     }
 287
 288     if( defined $config_file -> p_forward ){
 289       $orig_p_value = $config_file -> p_value;
 290       $config_file -> p_value( $config_file -> p_forward );
 291     }
 292
 293   }
 294
 295   $config_file -> search_direction( 'forward' );
 296
 297   $scm = tool::scm ->
 298       new ( eval( $common_options::parameters ),
 299             models      => $models_array,
 300             config_file => $config_file );
 301   open(CMD, ">", $scm -> directory . "/command.txt");
 302   print CMD $cmd_line, "\n";
 303   close(CMD);
 304
 305   $scm -> run;
 306
 307   #$scm -> print_results;
 308
 309   if( -e $options{'config_file'} ){
 310     if( defined $orig_ofv ){
 311       $config_file -> ofv_change( $orig_ofv );
 312     }
 313
 314     if( defined $orig_p_value ){
 315       $config_file -> p_value( $orig_p_value );
 316     }
 317
 318     if( defined $scm -> base_criteria_values ){
 319       $config_file -> base_criteria_values( @{$scm -> base_criteria_values}[0] );
 320     }
 321
 322     if( defined $scm -> included_relations ){
 323       $config_file -> included_relations( @{$scm -> included_relations}[0] );
 324     }
 325   }
 326 }
 327
 328 if( $direction eq 'backward' or $direction eq 'both' ){
 329
 330   if( -e $options{'config_file'} ){
 331     if( defined $config_file -> ofv_backward ){
 332       $config_file -> ofv_change( $config_file -> ofv_backward );
 333     }
 334
 335     if( defined $config_file -> p_backward ){
 336       $config_file -> p_value( $config_file -> p_backward );
 337     }
 338
 339   }
 340
 341   $config_file -> search_direction( 'backward' );
 342
 343   my $scm_back = tool::scm ->
 344       new ( eval( $common_options::parameters ),
 345 #           included_relations => $scm -> included_relations,
 346             directory   => ( defined $options{'backwards_dir'} and
 347                              $options{'backwards_dir'} ne '' ) ? $options{'backwards_dir'} : $config_file -> directory,
 348             models      => $models_array,
 349             config_file => $config_file );
 350
 351   ui -> print( category => 'scm',
 352                message => "Starting scm backward search" );
 353
 354   open(CMD, ">", $scm_back -> directory . "/command.txt");
 355   print CMD $cmd_line, "\n";
 356   close(CMD);
 357
 358   $scm_back -> run;
 359
 360   #$scm_back -> print_results;
 361 }
 362
 363 ui -> print( category => 'scm',
 364              message => "Done" );