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Summary

Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils - base class for
genebuild utility methods

Package variables

Included modules

Inherit

Exporter

Synopsis

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils qw(coord_string id 
                                                       empty_Object);

  or 

  use Bio::EnsEMBL::Analysis::Tools::GeneBuildUtils 

  to get all methods

Description

This is a base class for Utility modules for genebuilding and
other gene manupulation code. This module probably wont be used
direct outside of these classes but it can been if needed
It provides some simple functionality that all of the utility
modules need like id, to provide a sensible id string or
coord string to provide a basic, start, end, strand,
seq_region_name string for printing or removing databases connections
from objects
These modules are heavily based on the Utils modules which
can be found in EnsEMBL::Analysis::Pipeline::Tools

Methods

Methods description

  Arg [1]   : Bio::EnsEMBL::Feature
  Function  : returns a string with the start, end, strand
  and slice name that the feature is on delimited by spaces
  Returntype: string
  Exceptions: throws if no feature is passed in
  Example   :

  Arg [1]   : Bio::EnsEMBL::Storeable or an object which inherits from it
  Arg [2]   : Boolean, whether to remove the stable id from the given object
  Function  : remove the dbID, adaptor and if appropriate the stable id
  Returntype: Bio::EnsEMBL::Storeable
  Exceptions: n/a
  Example   : empty_Object($object);

  Arg [1]   : Bio::EnsEMBL::Feature
  Function  : returns a string containing an appropriate label
  for the feature
  Returntype: string
  Exceptions: none
  Example   :

  Arg [1]   : Bio::EnsEMBL::Feature
  Arg [2]   : Bio::EnsEMBL::Slice
  Function  : ensures the transcript within the slice, 
  completely on the lower end, it can overhang the upper end
  Returntype: boolean, 1 for pass 0 for fail ie(lies outside
                                                    of slice or
                                                    across lower 
                                                    boundary)
  Exceptions: none
  Example   :

Methods code

sub coord_string {

  my $feature = shift;
  my ($p, $f, $l) = caller;
  throw("Must be passed a feature") if(!$feature);
  my $string = $feature->start."\t".$feature->end."\t".$feature->strand."\t".$feature->slice->seq_region_name;
  return $string;

}

sub empty_Object {

  my ($object, $include_stable_id) = @_;
  $object->adaptor(undef);
  $object->dbID(undef);
  $object->stable_id(undef) if($object->can("stable_id") && 
                               $include_stable_id);
  return $object;

}

sub id {

  my $feature = shift;
  my $id;

  if($feature->can('stable_id') && $feature->stable_id){
    $id = $feature->stable_id;
  }elsif($feature->can('dbID') && $feature->dbID) {
    $id = $feature->dbID;
  }else{ 
    $id = 'no-id';
  }
  if($feature->can('biotype') && $feature->biotype){
    $id .= "_".$feature->biotype;
  }
  return $id;

}

sub lies_inside_of_slice {

  my ($feature, $slice) = @_;
  if($feature->start > $slice->length || 
     $feature->end < 1){
    warning(id($feature)." lies off edge if slice ".
            $slice->name);
    return 0;
  }
  if($feature->start < 1 && $feature->end > 1){
    warning(id($feature)." lies over lower boundary".
            " of slice ".$slice->name);
    return 0;
  }
  return 1;
}


1;

}

General documentation

please send any questions to ensembl-dev@ebi.ac.uk