bin/load_marker_locus_associations.pl

   1
   2 =head1 NAME
   3
   4 load_marker_locus_associations.pl - load associations between markers and loci.
   5
   6 =head1 DESCRIPTION
   7
   8 takes a file with two columns: locus names and marker names. Connects the two in the phenome.locus_marker table.
   9
  10 =head1 AUTHOR
  11
  12 Lukas Mueller <lam87@cornell.edu>
  13
  14 =cut
  15
  16 use strict;
  17 use warnings;
  18
  19 use Getopt::Std;
  20 use File::Slurp;
  21 use CXGN::DB::InsertDBH;
  22 use CXGN::Marker;
  23 use CXGN::Phenome::Locus;
  24
  25 our %args;
  26
  27 getopts('H:D:f:', \%args);
  28
  29 foreach (values %args) {
  30     print STDERR "param:  $_\n";
  31 }
  32
  33 my $dbh = CXGN::DB::InsertDBH->new( { dbname=> $args{D},
  34                                       dbhost=> $args{H}
  35                                     });
  36
  37 print STDERR "Reading file $args{f}\n";
  38 my @lmas = read_file($args{f});
  39
  40 foreach my $line (@lmas) {
  41     chomp($line);
  42     my ($locus_symbol, $marker_name)  = split /\t/, $line;
  43
  44     my $m = CXGN::Marker->new_with_name($dbh, $marker_name);
  45     if (!$m) { print STDERR "Marker not found: $marker_name. Skipping\n"; next; }
  46     my $marker_id = $m->marker_id();
  47
  48     my $h = $dbh -> prepare("SELECT locus_id FROM phenome.locus JOIN phenome.locus_alias using(locus_id) WHERE locus_name ilike ? OR locus_alias.alias ilike ? OR locus_symbol ilike ?");
  49
  50     $h->execute($locus_symbol, $locus_symbol, $locus_symbol);
  51
  52     my @ids = ();
  53     while (my ($locus_id) = $h->fetchrow_array()) {
  54         push @ids, $locus_id;
  55     }
  56     if (@ids > 1) {
  57         warn "There are more than 1 loci associated with SNP $marker_name\n";
  58     }
  59
  60     if (@ids == 0) {
  61         warn "Locus $locus_symbol not found.\n";
  62     }
  63     foreach my $locus_id (@ids) {
  64         my $l = CXGN::Phenome::Locus->new($dbh, $locus_id);
  65
  66         my $q = $dbh->prepare("INSERT INTO phenome.locus_marker (locus_id, marker_id) VALUES (?, ?)");
  67         $q -> execute($locus_id, $marker_id);
  68         print STDERR "Associated locus $locus_symbol ($locus_id) with marker $marker_name ($marker_id)\n";
  69     }
  70 }
  71
  72 $dbh->commit();
  73
  74
  75
  76