diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/RunnableDB/SetupMotifInference.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/RunnableDB/SetupMotifInference.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,81 @@
+=pod 
+
+=head1 NAME
+
+Bio::EnsEMBL::Funcgen::RunnableDB::SetupMotifInference
+
+=head1 DESCRIPTION
+
+'SetupMotifInference' 
+
+=cut
+
+
+package Bio::EnsEMBL::Funcgen::RunnableDB::SetupMotifInference;
+
+use warnings;
+use strict;
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
+use Data::Dumper;
+use POSIX qw(floor);
+
+
+use base ('Bio::EnsEMBL::Funcgen::RunnableDB::Motif');
+
+
+
+sub fetch_input {   # nothing to fetch... just the parameters...
+  my $self = shift @_;
+
+  $self->SUPER::fetch_input();
+
+  if(! -d $self->_output_dir){ 
+    system('mkdir -p '. $self->_output_dir) && throw "Error creating output dir ". $self->_output_dir;
+  }
+
+  return 1;
+}
+
+sub run {   # Create Subtasks of binsize peaks each, ignoring the last set of peaks ( < binsize peaks )
+  my $self = shift @_;
+
+  my $afa = $self->_efgdba()->get_AnnotatedFeatureAdaptor();
+  my @features = @{$afa->fetch_all_by_FeatureSets( [ $self->_feature_set ] )};
+  my $bins = POSIX::floor(scalar(@features)/$self->param('bin_size'));
+  if($bins < 1){ 
+    warn "Insuficient peaks. Please select a smaller bin size."; 
+  }
+  warn "Number of bins is $bins";
+
+  #Create jobs
+  my @bin_input_ids;
+  for (my $i=1;$i<=$bins;$i++){
+    #Need to add the specific file to the input_id...
+    my $new_input_id = eval($self->input_id);
+    $new_input_id->{"bin"} = $i;
+    push(@bin_input_ids, $new_input_id);
+  }
+  $self->_output_ids(\@bin_input_ids);
+
+  return 1;
+}
+
+
+sub write_output {  # Nothing is written at this stage (for the moment)
+  my $self = shift @_;
+
+  if($self->_output_ids && scalar($self->_output_ids)>0){
+    my ($converge_job_id) = @{ $self->dataflow_output_id($self->input_id, 3, { -semaphore_count => scalar(@{$self->_output_ids}) })  };
+    $self->dataflow_output_id($self->_output_ids, 2, { -semaphored_job_id => $converge_job_id });
+  }
+  return 1;
+
+}
+
+#Private getter / setter to the output ids
+sub _output_ids {
+  return $_[0]->_getter_setter('output_ids',$_[1]);
+}
+
+1;