query amigo

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1840 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/go_associations.pl

+#!/usr/local/bin/perl5.6.1
+
+use strict;
+
+BEGIN 
+{
+
+  my $configFile = "/nfs/pathdb/dev/go-cgi/config.pl";
+
+  if (-f $configFile) 
+  {
+    require $configFile;
+  }
+
+}
+
+use Getopt::Long;
+
+my $associations;
+my $definition;
+
+&GetOptions("assoc" => \$associations,
+            "def"   => \$definition);
+
+use GO::AppHandle;
+
+if(@ARGV == 0) 
+{
+ print "USAGE: go -def -assoc acc\n"; exit 0;
+}
+
+my $acc_num = $ARGV[0];
+
+my $dbname = $ENV{GO_DBNAME};
+my $dbport = $ENV{GO_DBPORT};
+my $dbhost = $ENV{GO_DBHOST};
+my $dbuser = $ENV{GO_DBUSER};
+
+if (not $dbname =~ /go\d/) 
+{
+  print STDERR "GO database name uncorrect, must be go1 or go2 !!";
+  exit 1;
+}
+
+my $apph = GO::AppHandle->connect (
+                                   -dbname => $dbname,
+                                   -dbport => $dbport,
+                                   -dbhost => $dbhost,
+                                   -dbuser => $dbuser,
+                                  ) 
+or die "can't connect to GO database, $dbname!!!\n";
+
+#my @accs = qw(O00221);
+my @accs;
+push(@accs, $acc_num);
+
+my @pqlist = map { {acc=>$_} } @accs;
+my $term_l = $apph->get_terms({products=>[@pqlist]});
+
+foreach my $term (@$term_l) 
+{
+  printf "%s; %s; ", $term->acc, $term->name;
+  if($associations)
+  {
+    foreach my $assoc (@{$term->selected_association_list || []}) 
+    {
+      my $gp = $assoc->gene_product;
+      my $ev_l = $assoc->evidence_list || [];
+      printf "%s; %s; %s; evidence=%s; %s;", 
+                        $gp->full_name, $gp->acc, $gp->symbol,
+                        join('; ', map {$_->code} @$ev_l), $gp->as_str;
+
+      foreach my $syn (@{$gp->synonym_list || []})
+      {
+        print " Synonym: $syn;";
+      }
+    }
+  }
+
+  if($definition)
+  {
+    printf " %s;", $term->definition;
+  }
+
+# printf "Synonyms:%s\n", join(", ", @{$term->synonym_list});
+
+  print "\n";
+
+}
+