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Summary

Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::Lagan

Package variables

Included modules

Inherit

Bio::EnsEMBL::Hive::Process

Synopsis

Description

This module interfaces the Hive and the Analsys systems: it allows to run Lagan jobs in an
ensembl-hive production systems. Jobs are run using the Bio::EnsEMBL::Analysis::Runnable::Lagan
module.

Methods

Methods description

    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for repeatmasker from the database
    Returns :   none
    Args    :   none

Methods code

sub build_tree_string {

  my $self = shift;
  my $tree_file = $self->tree_file;
  open F, $tree_file || throw("Can not open $tree_file");
  my $newick = "";
  while (<F>) {
    chomp;
    if (/^\s*(.*)\s*$/) {
      $newick .= $1;
    }
  }
  close F;

  my $tree = Bio::EnsEMBL::Compara::Graph::NewickParser::parse_newick_into_tree($newick);

  $self->update_node_names($tree);

  my $tree_string = $tree->newick_simple_format;

  $tree_string =~ s/:\d+\.\d+//g;
  $tree_string =~ s/[,;]/ /g;
  $tree_string =~ s/\"//g;

  $tree->release_tree;

  return $tree_string;

}

sub dumpFasta {

  my $self = shift;

#  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(1);

  my $sra = $self->{'comparaDBA'}->get_SyntenyRegionAdaptor;

  my $sr = $sra->fetch_by_dbID($self->synteny_region_id);

  my $idx = 1;

  foreach my $dfr (@{$sr->children}) {  
    my $file = $self->worker_temp_directory . "/seq" . $idx . ".fa";
    my $masked_file = $self->worker_temp_directory . "/seq" . $idx . ".fa.masked";
    $idx++;

    open F, ">$file" || throw("Couldn't open $file");
    open MF, ">$masked_file" || throw("Couldn't open $masked_file");

    # WARNING this is a hack. It won't work at all on self comparisons!!!
    # This will be more generic and fixed when the retain/release call will be
    # cleaned from the Node/Link/NestedSet code.
    # !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
    $self->{'_dnafrag_regions'}{$dfr->dnafrag_id} = $dfr;
    $dfr->retain;
    $dfr->disavow_parent;
    my $slice = $dfr->slice;
    print F ">DnaFrag" . $dfr->dnafrag_id . ".\n";
    print MF ">DnaFrag" . $dfr->dnafrag_id . ".\n";
    my $seq = $slice->seq;
    $seq =~ s/(.{80})/$1\n/g;
    chomp $seq;
    print F $seq,"\n";
    $seq = $slice->get_repeatmasked_seq->seq;
    $seq =~ s/(.{80})/$1\n/g;
    chomp $seq;
    print MF $seq,"\n";
  
    close F;
    close MF;

    push @{$self->fasta_files}, $file;
  }
#  $self->{'comparaDBA'}->dbc->disconnect_when_inactive(0);

  $sr->release_tree;

  if ($self->tree_file) {
    my $tree_string = $self->build_tree_string;
    $self->tree_string($tree_string);
  }
  return 1;

}

sub fasta_files {

  my $self = shift;

  $self->{'_fasta_files'} = [] unless (defined $self->{'_fasta_files'});

  if (@_) {
    my $value = shift;
    push @{$self->{'_fasta_files'}}, $value;
  }

  return $self->{'_fasta_files'};

}

sub fetch_input {

  my( $self) = @_;

  $self->{'comparaDBA'} = Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);
  $self->get_params($self->parameters);
  $self->get_params($self->input_id);

  $self->dumpFasta;

  return 1;

}

sub get_params {

  my $self         = shift;
  my $param_string = shift;

  return unless($param_string);
#   print("parsing parameter string : ",$param_string,"\n");

  my $params = eval($param_string);
  return unless($params);

  if(defined($params->{'synteny_region_id'})) {
    $self->synteny_region_id($params->{'synteny_region_id'});
  }
  if(defined($params->{'method_link_species_set_id'})) {
    $self->method_link_species_set_id($params->{'method_link_species_set_id'});
  }
  if(defined($params->{'tree_file'})) {
    $self->tree_file($params->{'tree_file'});
  }

  return 1;

}

sub method_link_species_set_id {

  my $self = shift;
  $self->{'_method_link_species_set_id'} = shift if(@_);
  return $self->{'_method_link_species_set_id'};
}

##########################################
#
# internal methods
#
##########################################

}

sub run {

  my $self = shift;

  my $runnable = new Bio::EnsEMBL::Analysis::Runnable::Lagan
    (-workdir => $self->worker_temp_directory,
     -fasta_files => $self->fasta_files,
     -tree_string => $self->tree_string,
     -analysis => $self->analysis);
  $self->{'_runnable'} = $runnable;
  $runnable->run_analysis;

}

sub synteny_region_id {

  my $self = shift;
  $self->{'_synteny_region_id'} = shift if(@_);
  return $self->{'_synteny_region_id'};

}

sub tree_file {

  my $self = shift;
  $self->{'_tree_file'} = shift if(@_);
  return $self->{'_tree_file'};

}

sub tree_string {

  my $self = shift;
  $self->{'_tree_string'} = shift if(@_);
  return $self->{'_tree_string'};

}

sub update_node_names {

  my $self = shift;
  my $tree = shift;
  my %gdb_id2dfr;
  foreach my $dfr (values %{$self->{'_dnafrag_regions'}}) {
    $gdb_id2dfr{$dfr->dnafrag->genome_db->dbID} = "DnaFrag".$dfr->dnafrag_id .".";
  }

  foreach my $leaf (@{$tree->get_all_leaves}) {
    if (defined $gdb_id2dfr{$leaf->name}) {
      $leaf->name($gdb_id2dfr{$leaf->name});
    } else {
      $leaf->disavow_parent;
      $tree = $tree->minimize_tree;
    }
  }
  if ($tree->get_child_count == 1) {
    my $child = $tree->children->[0];
    $child->parent->merge_children($child);
    $child->disavow_parent;
  }
  return $tree;
}

1;

}

sub write_output {

  my ($self) = @_;

  my $mlssa = $self->{'comparaDBA'}->get_MethodLinkSpeciesSetAdaptor;
  my $mlss = $mlssa->fetch_by_dbID($self->method_link_species_set_id);
  my $gaba = $self->{'comparaDBA'}->get_GenomicAlignBlockAdaptor;
  foreach my $gab (@{$self->{'_runnable'}->output}) {
    foreach my $ga (@{$gab->genomic_align_array}) {
      $ga->method_link_species_set($mlss);
      my $dfr = $self->{'_dnafrag_regions'}{$ga->dnafrag_id};
      $ga->dnafrag_id($dfr->dnafrag_id);
      $ga->dnafrag($dfr->dnafrag);
      $ga->dnafrag_start($dfr->dnafrag_start);
      $ga->dnafrag_end($dfr->dnafrag_end);
      $ga->dnafrag_strand($dfr->dnafrag_strand);
      $ga->level_id(1);
      $dfr->release;
      unless (defined $gab->length) {
        $gab->length(length($ga->aligned_sequence));
      }
    }
    $gab->method_link_species_set($mlss);
    $gaba->store($gab);
  }
  return 1;
}

##########################################
#
# getter/setter methods
# 
##########################################

#sub input_dir {
#  my $self = shift;
#  $self->{'_input_dir'} = shift if(@_);
#  return $self->{'_input_dir'};
#

}

General documentation

Javier Herrero
Abel Ureta-Vidal

Copyright (c) 2006. EnsEMBL Team
You may distribute this module under the same terms as perl itself

This modules is part of the EnsEMBL project ()
Questions can be posted to the ensembl-dev mailing list: ensembl-dev@ebi.ac.uk

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _