script/dump_smids.pl

   1
   2 use strict;
   3 use Getopt::Std;
   4 use SMIDDB;
   5 use JSON::XS;
   6
   7 our($opt_H, $opt_D, $opt_p);
   8 getopts('H:D:p:');
   9
  10 my $schema = SMIDDB->connect("dbi:Pg:host=$opt_H;dbname=$opt_D;user=postgres;password=$opt_p");
  11
  12 my $rs = $schema->resultset("SMIDDB::Result::Compound")
  13     ->search(
  14     {   'me.compound_id' => { '>' => 0 },
  15         'experiments.experiment_type' => 'ms_spectrum'
  16     },
  17     { join => 'experiments',
  18       '+select' => [ 'experiments.data' ],
  19       '+as' => [ 'data' ]
  20
  21
  22
  23     }
  24     );
  25
  26 while (my $row = $rs->next()) {
  27     my $data_json = $row->get_column('data');
  28     #    print STDERR $data_json;
  29
  30     my $data = undef;
  31     if ($data_json) {
  32         $data = JSON::XS->new->decode($data_json);
  33     }
  34
  35     my $spectrum = $data->{ms_spectrum_mz_intensity};
  36     my $adduct = $data->{ms_spectrum_adduct_fragmented};
  37
  38
  39
  40     print join("\t", $row->smid_id(), $row->smiles(), $adduct)."\n";
  41
  42     if (ref($spectrum) eq "ARRAY") {
  43         foreach my $line (@$spectrum) {
  44             print $line;
  45         }
  46     }
  47
  48
  49
  50
  51
  52
  53 }