Add prototype script for inferring interactions

We create genetic lethal interactions when appropriate single and
double alleles and annotation are in a session.

Refs pombase/pombase-chado#692

Author: kimrutherford

etc/make_interactions_from_double_mutants.pl

@@ -0,0 +1,140 @@
+#!/usr/bin/env perl
+
+# Create genotype-genotype interactions from double allele mutants
+#
+# See: https://github.com/pombase/pombase-chado/issues/692
+
+use strict;
+use warnings;
+use Carp;
+
+use utf8;
+
+use File::Basename;
+
+BEGIN {
+  my $script_name = basename $0;
+
+  if (-f $script_name && -d "../etc") {
+    # we're in the scripts directory - go up
+    chdir "..";
+  }
+};
+
+use lib qw(lib);
+
+use Canto::Config;
+use Canto::Track;
+use Canto::TrackDB;
+use Canto::Meta::Util;
+
+my $app_name = Canto::Config::get_application_name();
+
+$ENV{CANTO_CONFIG_LOCAL_SUFFIX} ||= 'deploy';
+
+my $suffix = $ENV{CANTO_CONFIG_LOCAL_SUFFIX};
+
+if (!Canto::Meta::Util::app_initialised($app_name, $suffix)) {
+  die "The application is not yet initialised, try running the canto_start " .
+    "script\n";
+}
+
+my $config = Canto::Config::get_config();
+
+push @{$config->{export_type_to_allele_type}->{nonsense_mutation}}, { name => 'nonsense mutation' };
+
+my $track_schema = Canto::TrackDB->new(config => $config);
+
+use utf8; use Canto::Track::OntologyLookup;
+
+my $lookup = Canto::Track::get_adaptor($config, "ontology");
+
+
+BEGIN { binmode STDOUT, ":encoding(UTF-8)"; }
+
+sub is_pop {
+  my $a = shift;
+  my $ag_rs = $a->genotypes();
+
+  for my $single_allele_genotype ($ag_rs->all()) {
+    return undef unless $single_allele_genotype->alleles()->count() == 1;
+
+    for my $single_allele_genotype_annotation ($single_allele_genotype->annotations()) {
+
+      my $term_ontid = $single_allele_genotype_annotation->data()->{term_ontid};
+      my $res = $lookup->lookup_by_id(id => $term_ontid,
+                                      include_subset_ids => 1);
+      if (grep { $_ eq 'is_a(FYPO:0002057)' } @{$res->{subset_ids}}
+) {
+        return $single_allele_genotype;
+      }
+    }
+  }
+
+  die "not pop\n";
+
+  return undef;
+};
+
+sub make_interaction {
+  my ($curs_schema, $interaction_type,
+      $double_mutant_genotype_annotation, $allele_1_genotype,
+      $allele_2_genotype) = @_;
+
+  my %create_args = (
+    interaction_type => $interaction_type,
+    primary_genotype_annotation_id =>
+    $double_mutant_genotype_annotation->genotype_annotation_id(),
+    genotype_a_id => $allele_1_genotype->genotype_id(),
+    genotype_b_id => $allele_2_genotype->genotype_id(),
+  );
+
+  print "created interaction\n";
+
+  $curs_schema->create_with_type('GenotypeInteraction', \%create_args);
+}
+
+my $proc = sub {
+  my $curs = shift;
+  my $curs_schema = shift;
+  my $track_schema = shift;
+
+  my $rs = $curs_schema->resultset("Annotation")
+    ->search({ type => "phenotype" });
+
+  while (defined (my $an = $rs->next())) {
+    my $data = $an->data();
+    next unless $data->{term_ontid} eq "FYPO:0002061";
+    my $genotype_annotations_rs = $an->genotype_annotations();
+    my $genotype_annotation = $genotype_annotations_rs->first();
+
+    if ($genotype_annotation->genotype_interactions()->count() > 0) {
+      next;
+    }
+
+    my $double_allele_genotype = $genotype_annotation->genotype();
+    my $alleles_rs = $double_allele_genotype->alleles();
+    next unless $alleles_rs->count() == 2;
+    my $allele_1 = $alleles_rs->next();
+    next unless $allele_1->type() eq "deletion";
+    my $allele_1_genotype = is_pop($allele_1);
+    next unless defined $allele_1_genotype;
+    my $allele_2 = $alleles_rs->next();
+    next unless $allele_2->type() eq "deletion";
+    my $allele_2_genotype = is_pop($allele_2);
+    next unless defined $allele_2_genotype;
+
+    print $curs->curs_key(), "\n";
+    make_interaction($curs_schema, 'Synthetic Growth Defect',
+                     $genotype_annotation, $allele_1_genotype,
+                     $allele_2_genotype);
+  }
+};
+
+my $transaction = sub {
+  Canto::Track::curs_map($config, $track_schema, $proc);
+};
+
+$track_schema->txn_do($transaction);
+
+