Raw content of Bio::EnsEMBL::Compara::RunnableDB::HclusterRun
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Compara::RunnableDB::HclusterRun
=cut
=head1 SYNOPSIS
my $aa = $sdba->get_AnalysisAdaptor;
my $analysis = $aa->fetch_by_logic_name('HclusterRun');
my $rdb = new Bio::EnsEMBL::Compara::RunnableDB::HclusterRun(
-input_id => "{'species_set'=>[1,2,3,14]}",
-analysis => $analysis);
$rdb->fetch_input
$rdb->run;
=cut
=head1 DESCRIPTION
This is a compara specific runnableDB, that based on an input_id
of arrayrefs of genome_db_ids, and from this species set relationship
it will search through the peptide_align_feature data and build
Hclusters and store them into a NestedSet datastructure.
This is the first step in the ProteinTree analysis production system.
=cut
=head1 CONTACT
Contact Albert Vilella on module implemetation/design detail: avilella@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.ac.uk
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::RunnableDB::HclusterRun;
use strict;
use Switch;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Compara::NestedSet;
use Bio::EnsEMBL::Compara::Homology;
use Bio::EnsEMBL::Compara::Graph::ConnectedComponents;
use Bio::EnsEMBL::Compara::MethodLinkSpeciesSet;
use Time::HiRes qw(time gettimeofday tv_interval);
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
sub fetch_input {
my( $self) = @_;
$self->{'species_set'} = undef;
$self->{'clusterset_id'} = 1;
$self->throw("No input_id") unless defined($self->input_id);
#create a Compara::DBAdaptor which shares the same DBI handle
#with the Pipeline::DBAdaptor that is based into this runnable
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);
$self->get_params($self->parameters);
my @species_set = @{$self->{'species_set'}};
$self->{'cluster_mlss'} = new Bio::EnsEMBL::Compara::MethodLinkSpeciesSet;
$self->{'cluster_mlss'}->method_link_type('PROTEIN_TREES');
my @genomeDB_set;
foreach my $gdb_id (@species_set) {
my $gdb = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($gdb_id);
throw("print gdb not defined for gdb_id = $gdb_id\n") unless (defined $gdb);
push @genomeDB_set, $gdb;
}
$self->{'cluster_mlss'}->species_set(\@genomeDB_set);
# $self->{gdba} = $self->{'comparaDBA'}->get_GenomeDBAdaptor;
# my $input_gdb_id = $self->input_id;
# my $gdb = $self->{gdba}->fetch_by_dbID($input_gdb_id);
# throw("no genome_db for $input_gdb_id") unless(defined($gdb));
# $self->{gdb} = $gdb;
return 1;
}
sub get_params {
my $self = shift;
my $param_string = shift;
return if ($param_string eq "1");
return unless($param_string);
print("parsing parameter string : ",$param_string,"\n");
my $params = eval($param_string);
return unless($params);
foreach my $key (keys %$params) {
print(" $key : ", $params->{$key}, "\n");
}
if (defined $params->{'species_set'}) {
$self->{'species_set'} = $params->{'species_set'};
}
if (defined $params->{'fasta_dir'}) {
$self->{'fasta_dir'} = $params->{'fasta_dir'};
}
if (defined $params->{'outgroups'}) {
foreach my $outgroup (@{$params->{'outgroups'}}) {
$self->{outgroups}{$outgroup} = 1;
}
}
if (defined $params->{'max_gene_count'}) {
$self->{'max_gene_count'} = $params->{'max_gene_count'};
}
print("parameters...\n");
printf(" fasta_dir : %d\n", $self->{'fasta_dir'});
printf(" species_set : (%s)\n", join(',', @{$self->{'species_set'}}));
printf(" outgroups : (%s)\n", join(',', keys %{$self->{'outgroups'}}));
printf(" max_gene_count : %d\n", $self->{'max_gene_count'});
return;
}
sub run
{
my $self = shift;
$self->gather_input();
$self->run_hcluster();
return 1;
}
sub write_output {
my $self = shift;
$self->store_clusters();
$self->dataflow_clusters;
# modify input_job so that it now contains the clusterset_id
my $outputHash = {};
$outputHash = eval($self->input_id) if(defined($self->input_id) && $self->input_id =~ /^\s*\{.*\}\s*$/);
$outputHash->{'clusterset_id'} = $self->{'clusterset_id'};
my $output_id = $self->encode_hash($outputHash);
return 1;
}
sub store_clusters {
my $self = shift;
$self->{retry} = $self->input_job->retry_count if ($self->input_job->retry_count > 10);
my $mlssDBA = $self->{'comparaDBA'}->get_MethodLinkSpeciesSetAdaptor;
my $pafDBA = $self->{'comparaDBA'}->get_PeptideAlignFeatureAdaptor;
my $treeDBA = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;
my $starttime = time();
my $clusterset;
$clusterset = $treeDBA->fetch_node_by_node_id($self->{'clusterset_id'});
if (!defined($clusterset)) {
$self->{'ccEngine'} = new Bio::EnsEMBL::Compara::Graph::ConnectedComponents;
$clusterset = $self->{'ccEngine'}->clusterset;
throw("no clusters generated") unless($clusterset);
$clusterset->name("PROTEIN_TREES");
$treeDBA->store_node($clusterset);
printf("root_id %d\n", $clusterset->node_id);
$self->{'clusterset_id'} = $clusterset->node_id;
$mlssDBA->store($self->{'cluster_mlss'});
printf("MLSS %d\n", $self->{'cluster_mlss'}->dbID);
}
my $mlss_id = $self->{'cluster_mlss'}->dbID;
$mlss_id = $self->{comparaDBA}->get_MethodLinkSpeciesSetAdaptor->fetch_by_method_link_type_GenomeDBs($self->{cluster_mlss}->method_link_type,$self->{cluster_mlss}->species_set)->dbID unless (defined($mlss_id));
my $filename;
if (defined($self->{retry})) {
my $fasta_dir = $self->{fasta_dir};
$filename = $fasta_dir . "/" . "hcluster.out";
} else {
$filename = $self->worker_temp_directory . "/" . "hcluster.out";
}
$self->{memberDBA} = $self->{'comparaDBA'}->get_MemberAdaptor;
$self->{treeDBA} = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;
open FILE, "$filename" or die $!;
my $counter=1;
while (<FILE>) {
# 0 0 0 1.000 2 1 697136_68,
# 1 0 39 1.000 3 5 1213317_31,1135561_22,288182_42,426893_62,941130_38,
chomp $_;
my ($cluster_id, $dummy1, $dummy2, $dummy3, $dummy4, $dummy5, $cluster_list) = split("\t",$_);
next if ($dummy5 < 2);
$cluster_list =~ s/\,^//;
my @cluster_list = split(",",$cluster_list);
# If it's a singleton, we don't store it as a protein tree
next if (2 > scalar(@cluster_list));
if($counter % 20 == 0) { printf("%10d clusters\n", $counter); }
$counter++;
my $cluster = new Bio::EnsEMBL::Compara::NestedSet;
$clusterset->add_child($cluster);
my $already_present;
my $number_raw_cluster = scalar(@cluster_list);
my $number_filtered_cluster = 0;
if (defined($self->{retry}) && $self->{retry} >= 20) {
foreach my $member_hcluster_id (@cluster_list) {
my ($pmember_id,$genome_db_id) = split("_",$member_hcluster_id);
my $aligned_member = $self->{treeDBA}->fetch_AlignedMember_by_member_id_root_id($pmember_id, 1);
if (defined($aligned_member)) {
$already_present->{$aligned_member->member_id} = 1;
}
}
next if ($number_raw_cluster == (scalar keys %$already_present));
}
$DB::single=1;1;
foreach my $member_hcluster_id (@cluster_list) {
my ($pmember_id,$genome_db_id) = split("_",$member_hcluster_id);
if (defined($self->{retry}) && $self->{retry} >= 20) {
my $member = $self->{memberDBA}->fetch_by_dbID($pmember_id);
my $longest_member = $member->gene_member->get_longest_peptide_Member;
next unless ($longest_member->member_id eq $member->member_id);
next if (defined($already_present->{$member->member_id}));
}
my $node = new Bio::EnsEMBL::Compara::NestedSet;
$node->node_id($pmember_id);
$cluster->add_child($node);
#leaves are NestedSet objects, bless to make into AlignedMember objects
bless $node, "Bio::EnsEMBL::Compara::AlignedMember";
#the building method uses member_id's to reference unique nodes
#which are stored in the node_id value, copy to member_id
$node->member_id($node->node_id);
$node->method_link_species_set_id($mlss_id);
}
# Store the cluster
$treeDBA->store($cluster);
#calc residue count total
my $leafcount = scalar(@{$cluster->get_all_leaves});
$cluster->store_tag('gene_count', $leafcount);
if (defined($self->{retry}) && $self->{retry} >= 20) {
$cluster->store_tag('readded_cluster', 1);
print STDERR "Re-adding cluster ", $cluster->node_id, "with $leafcount members\n";
}
# $cluster->store_tag('include_brh', $self->{'include_brh'});
# $cluster->store_tag('bsr_threshold', $self->{'bsr_threshold'});
}
return 1;
}
##########################################
#
# internal methods
#
##########################################
sub gather_input {
my $self = shift;
my $starttime = time();
return undef if ($self->input_job->retry_count > 10);
my $fasta_dir = $self->{fasta_dir};
my $output_dir = $self->worker_temp_directory;
my $cmd;
print "gathering input in $output_dir\n" if ($self->debug);
$cmd ="cat $fasta_dir/*.hcluster.cat > $output_dir/hcluster.cat";
unless(system($cmd) == 0) {
$self->check_job_fail_options;
throw("error gathering category files for Hcluster, $!\n");
}
printf("%1.3f secs to gather category entries\n", (time()-$starttime));
$cmd ="cat $fasta_dir/*.hcluster.txt > $output_dir/hcluster.txt";
unless(system($cmd) == 0) {
$self->check_job_fail_options;
throw("error gathering distance files for Hcluster, $!\n");
}
printf("%1.3f secs to gather distance entries\n", (time()-$starttime));
}
sub run_hcluster {
my $self = shift;
my $starttime = time();
return undef if ($self->input_job->retry_count > 10);
my $hcluster_executable = $self->analysis->program_file;
unless (-e $hcluster_executable) {
if (`uname -m` =~ /ia64/) {
$hcluster_executable
= "/nfs/acari/avilella/src/treesoft/trunk/ia64/hcluster/hcluster_sg";
} else {
$hcluster_executable
= "/nfs/acari/avilella/src/treesoft/trunk/hcluster/hcluster_sg";
}
}
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);
my $cmd = $hcluster_executable;
my $max_count = int($self->{'max_gene_count'}/2); # hcluster can joint up to (max_count+(max_count-1))
$cmd .= " ". "-m $max_count -w 0 -s 0.34 -O ";
$cmd .= "-C " . $self->worker_temp_directory . "hcluster.cat ";
$cmd .= "-o " . $self->worker_temp_directory . "hcluster.out ";
$cmd .= " " . $self->worker_temp_directory . "hcluster.txt";
print("Ready to execute:\n") if($self->debug);
print("$cmd\n") if($self->debug);
unless(system($cmd) == 0) {
$self->check_job_fail_options;
throw("error running hcluster, $!\n");
}
$self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);
printf("%1.3f secs to execute\n", (time()-$starttime));
return 1;
}
sub dataflow_clusters {
my $self = shift;
my $treeDBA = $self->{'comparaDBA'}->get_ProteinTreeAdaptor;
my $starttime = time();
my $clusterset;
$clusterset = $treeDBA->fetch_node_by_node_id($self->{'clusterset_id'});
if (!defined($clusterset)) {
$clusterset = $self->{'ccEngine'}->clusterset;
}
my $clusters = $clusterset->children;
foreach my $cluster (@{$clusters}) {
my $output_id = sprintf("{'protein_tree_id'=>%d, 'clusterset_id'=>%d}",
$cluster->node_id, $clusterset->node_id);
if (defined($self->{retry})) {
my $readded_cluster_tag = $cluster->get_tagvalue("readded_cluster");
next unless (1 == $readded_cluster_tag); # Will skip flow unless is one of the readded
}
$self->dataflow_output_id($output_id, 2);
}
}
sub check_job_fail_options
{
my $self = shift;
if($self->input_job->retry_count >= 5) {
$self->input_job->update_status('FAILED');
throw("HclusterRun job failed >=5 times: try something else and FAIL it");
}
}
1;
]]>