bin/nonpb

   1 #!/usr/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 model;
  11 use tool::nonpb;
  12 use strict;
  13 use debug;
  14 use Getopt::Long;
  15 use common_options;
  16
  17 my $cmd_line = $0 . " " . join( " ", @ARGV );
  18
  19 ## Configure the command line parsing
  20 Getopt::Long::config("auto_abbrev");
  21
  22 my %options;
  23 ## Declare the options
  24
  25 my %required_options = ( 'samples:i' => '200');
  26 #my %optional_options = ( 'alternative_models:s' => 'alt1.mod,alt2.mod,...',
  27 #                        'ref_ofv:i' => '500',
  28 #                        'estimate_simulation!' => '1' );
  29
  30 my %optional_options = ("etas:i"=>'',
  31                         "lst:s"=>''
  32                         );
  33
  34 my $res = GetOptions( \%options,
  35                       @common_options::get_opt_strings,
  36                       keys(%required_options),
  37                       keys(%optional_options) );
  38 exit unless $res;
  39
  40 common_options::set_globals( \%options );
  41 common_options::get_defaults( \%options, 'nonpb' );
  42 common_options::sanity_checks( \%options, 'nonpb' );
  43
  44 my %help_text;
  45
  46 $help_text{Pre_help_message} = <<'EOF';
  47   nonpb
  48
  49     Perl script for Non-Parametric Bootstrap.
  50
  51   Usage:
  52 EOF
  53
  54 $help_text{Options} = <<'EOF';
  55     Options:
  56
  57       The options are given here in their long form. Any option may be
  58       abbreviated to any nonconflicting prefix. The -threads option
  59       may be abbreviated to -t(or even -thr) but -debug may not be
  60       abbreviated to -d because it conflicts with -debug_packages and
  61       -debug_subroutines.
  62
  63       The following options are valid:
  64 EOF
  65
  66 $help_text{-h} = <<'EOF';
  67       -h | -?
  68
  69       With -h or -? nonpb will print a list of options and exit.
  70 EOF
  71
  72 $help_text{-help} = <<'EOF';
  73       -help
  74
  75       With -help nonpb will print this, longer, help message.
  76 EOF
  77
  78 $help_text{-samples} = <<'EOF';
  79       -samples=N
  80
  81       Required option. The number of samples for the bootstrap.
  82
  83 EOF
  84
  85 $help_text{-etas} = <<'EOF';
  86       -etas=N
  87
  88       Optional, the number of ETAs (starting with ETA1) for which the
  89       nonp_bootstrap should be run. Default is all ETAs.
  90
  91 EOF
  92
  93 $help_text{-lst} = <<'EOF';
  94       -lst=<filename>
  95
  96       Optional, the lst-file from where to read initial parameter estimates.
  97       Default is the same name as the model file but with .mod replaced with .lst.
  98 EOF
  99
 100
 101 $help_text{Post_help_message} = <<'EOF';
 102       Also see 'execute -help' for a description of common options.
 103 EOF
 104
 105 common_options::online_help( 'nonpb', \%options, \%help_text, \%required_options, \%optional_options);
 106
 107 ## Check that we do have a model file
 108 if ( scalar(@ARGV) < 1 ) {
 109   print "A simulation model file must be specified. Use 'nonpb -h' for help.\n";
 110   exit;
 111 }
 112
 113 if( scalar(@ARGV) > 1 ){
 114   print "NONPB can only handle one modelfile, you listed: ",
 115   join(',',@ARGV),". Use 'nonpb -h' for help.\n";die;
 116   exit;
 117 }
 118
 119 my $lst_file;
 120 if (defined $options{'lst'}){
 121   $lst_file=$options{'lst'};
 122 } else {
 123   #assume modelfile ends with .mod
 124   $lst_file = (substr ($ARGV[0],0,-3)).'lst'; #keep from beginning, skip last four characters
 125   unless ( -e $lst_file ){
 126     print "When option -lst is omitted, the name of the lst-file is assumed to be the same\n".
 127         "as the modelfile except that the last three letters are lst. Cannot find file $lst_file\.";
 128     exit;
 129   }
 130 }
 131
 132 #unless ( defined $options{'clean'} ){
 133   # Clean may be changed by default
 134 #  $options{'clean'} = 1;
 135 #}
 136
 137 ui -> category( 'nonpb' );
 138 ui -> silent(1) if( $options{'silent'} );
 139
 140 debug -> level( $options{'debug'} );
 141 debug -> package( $options{'debug_package'} );
 142 debug -> subroutine( $options{'debug_subroutine'} );
 143 debug -> warn_with_trace( $options{'warn_with_trace'} );
 144
 145 my $eval_string = common_options::model_parameters(\%options);
 146
 147 my $model = model -> new ( eval( $eval_string ),
 148                            filename                    => $ARGV[0],
 149                            ignore_missing_output_files => 1 );
 150
 151 my $nonpb = tool::nonpb ->
 152     new ( eval( $common_options::parameters ),
 153           models             => [$model],
 154           lst_file           => $lst_file,
 155           samples            => $options{'samples'},
 156           etas               => $options{'etas'});
 157
 158
 159 open(CMD, ">", $nonpb -> directory . "/command.txt");
 160 print CMD $cmd_line, "\n";
 161 close(CMD);
 162
 163 unless( -d $nonpb -> directory . "/intermediate_files" ){
 164   mkdir( $nonpb -> directory . "/intermediate_files" );
 165 }
 166 unless( -d $nonpb -> directory . "/result_files" ){
 167   mkdir( $nonpb -> directory . "/result_files" );
 168 }
 169
 170 #this is sec 1 and 2 of URS nonp_bootstrap_v2
 171 #individual step 1a,1b,2a done by bootstrap tool, can simply collect results
 172 #from bootstrap object
 173
 174 #1.0
 175
 176 ##do the bootstrap in a specific sub-directory of  nonpb_dirY : 'bootstrap'
 177 #must carry a whole hash of options here, can lump them together according to Pontus, how???.
 178 #ask Pontus about not having to list all options
 179
 180 chdir( $nonpb -> directory );
 181 my $type = defined $options{'bca'} ? 'bca' : undef;
 182 my $bs = tool::bootstrap ->
 183     new ( eval( $common_options::parameters ),
 184           directory => 'bootstrap',
 185           models        => [ $model ],
 186           samples       => $options{'samples'}
 187           #the hash!!! Ask Pontus....
 188           );
 189 $bs -> run;
 190 $bs -> prepare_results();
 191 $bs -> print_results();
 192
 193 #Does this work? I set model array here and not in 'new' since
 194 #must have bootstrap model array first. Want to have
 195 #nonpb directory before running bootstrap, therefore do new nonpb before bootstrap
 196 #use function here instead of assignment???
 197 $nonpb -> {'start_bs_models'} = $bs -> {'prepared_models'}[0]{'own'}; #bara referens?
 198
 199 $bs = undef;
 200
 201 $nonpb -> run;
 202
 203 #open( TMP, ">", 'ofv.done' );
 204 #print TMP "1";
 205 #close( TMP );
 206
 207
 208 #$nonpb -> prepare_results;
 209 #$nonpb -> print_results;
 210