cgi-bin/phenome/pop_download.pl

   1 #!/usr/bin/perl -wT
   2
   3 =head1 DESCRIPTION
   4 A small script for downloading population
   5 phenotype raw data in tab delimited format.
   6
   7 =head1 AUTHOR(S)
   8
   9 Isaak Y Tecle (iyt2@cornell.edu)
  10
  11 =cut
  12
  13 use strict;
  14
  15 use CXGN::DB::Connection;
  16 use CXGN::Phenome::Population;
  17 use CXGN::Phenome::Individual;
  18 use CXGN::Scrap;
  19
  20 my $scrap = CXGN::Scrap->new();
  21 my $dbh   = CXGN::DB::Connection->new();
  22
  23 my $population_id = $scrap->get_encoded_arguments("population_id");
  24
  25 my $pop = CXGN::Phenome::Population->new( $dbh, $population_id );
  26 my $name = $pop->get_name();
  27
  28 print
  29 "Pragma: \"no-cache\"\nContent-Disposition:filename=phenotype_data_${population_id}.txt\nContent-type:application/data\n\n";
  30
  31 #print "Content-Type: text/plain\n\n";
  32
  33 print "Phenotype data for $name\n\n\n";
  34
  35
  36 my @individuals = $pop->get_individuals();
  37
  38 my ( @pop_id, @name, @obs_id, @cvterm, @definition, @value );
  39
  40 my $individual_obj = $individuals[1];
  41
  42 my $indv_id = $individual_obj->get_individual_id();
  43
  44 my @cvterms = $individual_obj->get_unique_cvterms($indv_id);
  45
  46 print "Lines \t";
  47 print join( "\t", @cvterms );
  48
  49 my ( $pop_id, $pop_name, $ind_id, $ind_name, $obs_id, $cvterm, $definition,
  50      $value )
  51   = $pop->get_pop_raw_data();
  52
  53 my $old_ind_id = "";
  54
  55 for ( my $i = 0 ; $i < @$pop_id ; $i++ )
  56 {
  57     if ( $old_ind_id ne $ind_id->[$i] )
  58     {
  59
  60         print "\n$ind_name->[$i]\t";
  61     }
  62
  63     foreach my $t (@cvterms)
  64     {
  65         my $term = $cvterm->[$i];
  66         if ( $t =~ /^$term$/i )
  67         {
  68             print "$value->[$i]\t";
  69         }
  70     }
  71     $old_ind_id = $ind_id->[$i];
  72 }
  73