bin/remove_parents.pl

   1
   2 use strict;
   3 use Getopt::Std;
   4 use DBI;
   5 use Bio::Chado::Schema;
   6
   7 our ($opt_H, $opt_D);
   8 getopts('H:D:');
   9
  10 my $file = shift;
  11
  12 print "Password for $opt_H / $opt_D: \n";
  13 my $pw = <>;
  14 chomp($pw);
  15
  16 print STDERR "Connecting to database...\n";
  17 my $dsn = 'dbi:Pg:database='.$opt_D.";host=".$opt_H.";port=5432";
  18
  19 my $dbh = DBI->connect($dsn, "postgres", $pw);
  20
  21 print STDERR "Connecting to DBI schema...\n";
  22 my $bcs_schema = Bio::Chado::Schema->connect($dsn, "postgres", $pw);
  23
  24 my $female_parent_type_id = $bcs_schema->resultset("Cv::Cvterm")->find( { name => "female_parent" })->cvterm_id();
  25
  26 my $male_parent_type_id = $bcs_schema->resultset("Cv::Cvterm")->find( { name=> "male_parent" })->cvterm_id();
  27
  28 my $total_count = 0;
  29
  30 open(my $F, "<", $file) || die " Can't open file $file\n";
  31 while (<$F>) {
  32     chomp;
  33
  34     my $stock = $_;
  35     $stock =~ s/\r//g;
  36     if (!$stock) {
  37         next();
  38     }
  39
  40     print STDERR "Processing $stock\n";
  41
  42     my $stock_row = $bcs_schema->resultset("Stock::Stock")->find( { uniquename => $stock });
  43
  44     if (!$stock_row) {
  45         print STDERR "Could not find stock $stock. Skipping...\n";
  46         next;
  47     }
  48
  49
  50     my $parent_rs = $bcs_schema->resultset("Stock::StockRelationship")->search( { object_id => $stock_row->stock_id(), type_id => { -in => [ $female_parent_type_id, $male_parent_type_id] } });
  51
  52     print STDERR "Found ".$parent_rs->count()." parents for stock $stock\n";
  53
  54     while (my $p = $parent_rs->next()) {
  55         print STDERR "Removing parent with id ".$p->subject_id()."...\n";
  56         $p->delete();
  57         $total_count++;
  58     }
  59 }
  60
  61 print STDERR "Done. Total relationships deleted: $total_count.\n";
  62
  63
  64