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#!/usr/bin/perl
# assumes empty password--that should be fixed
use strict;
use DBI;
use Bio::OntologyIO;
use Bio::Ontology::TermFactory;
my ($user, $dbname, $cvname) = @ARGV;
die "USAGE: $0 <username> <dbname> <cvname>" unless $user and $dbname and $cvname;
my $db = DBI->connect("dbi:Pg:dbname=$dbname",$user,'');
my $sth_objects = $db->prepare("select object_id from cvterm_relationship where subject_id = ? and type_id = ?");
my $sth_subjects = $db->prepare("select subject_id from cvterm_relationship where object_id = ? and type_id = ?");
my $sth_allobjects = $db->prepare("select object_id from cvterm_relationship where subject_id = ?");
my $sth_allsubjects = $db->prepare("select subject_id from cvterm_relationship where object_id = ?");
my %type;
my %subject;
my %object;
my %black;
my(%root,%leaf);
my %sot;
my $sth_type = $db->prepare("select cvterm_id from cvterm where cv_id = (select cv_id from cv where name = 'Relationship Ontology')");
$sth_type->execute;
while(my $type_id = $sth_type->fetchrow){
$type{$type_id}++;
}
my %cvterm;
my $sth_cvterm = $db->prepare("select cvterm_id from cvterm");
$sth_cvterm->execute;
while(my $cvterm_id = $sth_cvterm->fetchrow_array){
$cvterm{$cvterm_id}++;
}
my $cv_id;
warn "select cv_id from cv where name = '$cvname'";
my $sth_cv = $db->prepare("select cv_id from cv where name = '$cvname'");
$sth_cv->execute;
while(my $cv = $sth_cv->fetchrow_hashref){
$cv_id = $cv->{cv_id};
}
die "no cv_id for '$cvname'" unless defined $cv_id;
#my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship");
my $sth_cvterm_relationship = $db->prepare("select subject_id,type_id,object_id from cvterm_relationship,cvterm where cvterm_relationship.subject_id = cvterm.cvterm_id and cvterm.cv_id = $cv_id");
$sth_cvterm_relationship->execute;
while(my $cvterm_relationship = $sth_cvterm_relationship->fetchrow_hashref){
$subject{$cvterm_relationship->{subject_id}}++;
$object{$cvterm_relationship->{object_id}}++;
$sot{$cvterm_relationship->{subject_id}}{$cvterm_relationship->{object_id}}{$cvterm_relationship->{type_id}}++;
}
foreach my $cvterm (keys %cvterm){
$root{$cvterm}++ if(!$subject{$cvterm} and $object{$cvterm});
$leaf{$cvterm}++ if( $subject{$cvterm} and !$object{$cvterm});
}
my %leafbak = %leaf;
%sot = ();
while(keys %leaf){
foreach my $leaf (keys %leaf){
foreach my $type (keys %type){
recurse([$leaf],$type,1);
}
delete $leaf{$leaf};
}
# print "**************************************\n";
}
%leaf = %leafbak;
while(keys %leaf){
foreach my $leaf (keys %leaf){
recurse([$leaf],undef,1);
delete $leaf{$leaf};
}
# print "**************************************\n";
}
sub recurse {
my($subjects,$type,$dist) = @_;
my $subject = $subjects->[-1];
# print $subject,"\n";
my @objects = objects($subject,$type);
if(!@objects){
$leaf{$subject}++;
return;
}
foreach my $object (@objects){
my $tdist = $dist;
foreach my $s (@$subjects){
next if $sot{$s}{$object}{$type}{$tdist};
$sot{$s}{$object}{$type}{$tdist}++;
# print $tdist,"\t"x$dist,"\t",$s,"\t",$object,"\t",$type||'transitive',"\n";
if(defined $type){
print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
($s,$object,$type,$cv_id,$tdist);\n";
my $ttdist = -1 * $tdist;
print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
($object,$subject,$type,$cv_id,$ttdist);\n";
} else {
print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
($s,$object,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,$tdist);\n";
print "insert into cvtermpath (subject_id,object_id,type_id,cv_id,pathdistance) values
($object,$subject,(select cvterm_id from cvterm where name = 'OBO_REL:0001'),$cv_id,-$tdist);\n";
}
$tdist--;
}
$tdist = $dist;
recurse([@$subjects,$object],$type,$dist+1);
}
}
#-------------------
sub objects {
my($subject,$type) = @_;
#warn $subject;
my @objects;
if(defined($type)){
$sth_objects->execute($subject,$type);
while(my $object = $sth_objects->fetchrow_array){
push @objects, $object;
}
} else {
$sth_allobjects->execute($subject);
while(my $object = $sth_allobjects->fetchrow_array){
push @objects, $object;
}
}
return @objects;
}
sub subjects {
my($object,$type) = @_;
my @subjects;
if(defined($type)){
$sth_subjects->execute($object,$type);
while(my $subject = $sth_subjects->fetchrow_array){
push @subjects, $subject;
}
} else {
$sth_allsubjects->execute($object);
while(my $subject = $sth_allsubjects->fetchrow_array){
push @subjects, $subject;
}
}
return @subjects;
}
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