Bio::Coordinate::GeneMapper(3)

NAME
Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems

SYNOPSIS
  use Bio::Coordinate::GeneMapper;

  # get a Bio::RangeI representing the start, end and strand of the CDS
  # in chromosomal (or entry) coordinates
  my $cds;

  # get a Bio::Location::Split or an array of Bio::LocationI objects
  # holding the start, end and strand of all the exons in chromosomal
  # (or entry) coordinates
  my $exons;

  # create a gene mapper and set it to map from chromosomal to cds coordinates
  my $gene = Bio::Coordinate::GeneMapper->new(-in   =>'chr',
                                              -out  =>'cds',
                                              -cds  =>$cds,
                                              -exons=>$exons
                                             );

  # get a a Bio::Location or sequence feature in input (chr) coordinates
  my $loc;

  # map the location into output coordinates and get a new location object
  $newloc = $gene->map($loc);

DESCRIPTION
Bio::Coordinate::GeneMapper is a module for simplifying the mappings of coodinate locations between various gene related locations in human genetics. It also adds a special human genetics twist to coordinate systems by making it possible to disable the use of zero (0). Locations before position one start from -1. See method nozero.

It understands by name the following coordinate systems and mapping between them:

                          peptide (peptide length)
                             ^
                             | -peptide_offset
                             |
                    frame  propeptide (propeptide length)
                        ^    ^
                         \   |
             translate    \  |
                           \ |
                            cds  (transcript start and end)
                             ^
      negative_intron        | \
              ^              |  \  transcribe
               \             |   \
              intron        exon  \
               ^   ^         ^     /
      splice    \   \      / |    /
                 \   \    /  |   /
                  \   inex   |  /
                   \    ^    | /
                    \    \   |/
                     ----- gene (gene_length)
                             ^
                             | - gene_offset
                             |
                            chr (or entry)

This structure is kept in the global variable $DAG which is a representation of a Directed Acyclic Graph. The path calculations traversing this graph are done in a helper class. See Bio::Coordinate::Graph.

Of these, two operations are special cases, translate and splice. Translating and reverse translating are implemented as internal methods that do the simple 1<->3 conversion. Splicing needs additional information that is provided by method exons which takes in an array of Bio::LocationI objects.

Most of the coordinate system names should be selfexplanatory to anyone familiar with genes. Negative intron coordinate system is starts counting backwards from -1 as the last nucleotide in the intron. This used when only exon and a few flanking intron nucleotides are known.

This class models coordinates within one transcript of a gene, so to tackle multiple transcripts you need several instances of the class. It is therefore valid to argue that the name of the class should be TranscriptMapper. GeneMapper is a catchier name, so it stuck.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing lists Your participation is much appreciated.

  bioperl-l@bioperl.org                 - General discussion
  http://bio.perl.org/MailList.html     - About the mailing lists

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHOR - Heikki Lehvaslaiho
Email: heikki@ebi.ac.uk Address:

     EMBL Outstation, European Bioinformatics Institute
     Wellcome Trust Genome Campus, Hinxton
     Cambs. CB10 1SD, United Kingdom

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

  in
 Title   : in
 Usage   : $obj->in('peptide');
 Function: Set and read the input coordinate system.
 Example :
 Returns : value of input system
 Args    : new value (optional)

  out
 Title   : out
 Usage   : $obj->out('peptide');
 Function: Set and read the output coordinate system.
 Example :
 Returns : value of output system
 Args    : new value (optional)

  strict
 Title   : strict
 Usage   : $obj->strict('peptide');
 Function: Set and read whether strict boundaried of coordinate
           systems are enforced.
           When strict is on, the end of the coordinate range must be defined.
 Example :
 Returns : boolean
 Args    : boolean (optional)

  nozero
 Title   : nozero
 Usage   : $obj->nozero(1);
 Function: Flag to disable the use of zero in the input,
           output or both coordinate systems. Use of coordinate
           systems without zero is a peculiarity  common in
           human genetics community.
 Example :
 Returns : 0 (default), or 'in', 'out', 'in&out'
 Args    : 0 (default), or 'in', 'out', 'in&out'

  graph
 Title   : graph
 Usage   : $obj->graph($new_graph);
 Function: Set and read the graph object representing relationships
           between coordinate systems
 Example :
 Returns : Bio::Coordinate::Graph object
 Args    : new Bio::Coordinate::Graph object (optional)

  peptide
 Title   : peptide
 Usage   : $obj->peptide_offset($peptide_coord);
 Function: Read and write the offset of peptide from the start of propeptide
           and peptide length
 Returns : a Bio::Location::Simple object
 Args    : a Bio::LocationI object

  peptide_offset
 Title   : peptide_offset
 Usage   : $obj->peptide_offset(20);
 Function: Set and read the offset of peptide from the start of propeptide
 Returns : set value or 0
 Args    : new value (optional)

  peptide_length
 Title   : peptide_length
 Usage   : $obj->peptide_length(20);
 Function: Set and read the offset of peptide from the start of propeptide
 Returns : set value or 0
 Args    : new value (optional)

  exons
 Title   : exons
 Usage   : $obj->exons(@exons);
 Function: Set and read the offset of CDS from the start of transcipt
           You do not have to sort the exons before calling this method as
           they will be sorted automatically.
           If you have not defined the CDS, is will be set to span all
           exons here.
 Returns : array of Bio::LocationI exons in genome coordinates or 0
 Args    : array of Bio::LocationI exons in genome (or entry) coordinates

  _clone_loc
 Title   : _clone_loc
 Usage   : $copy_of_loc = $obj->_clone_loc($loc);
 Function: Make a deep copy of a simple location
 Returns : a Bio::Location::Simple object
 Args    : a Bio::Location::Simple object to be cloned

  cds
 Title   : cds
 Usage   : $obj->cds(20);
 Function: Set and read the offset of CDS from the start of transcipt

           Simple input can be an integer which gives the start of the
           coding region in genomic coordinate. If you want to provide
           the end of the coding region or indicate the use of the
           opposite strand, you have to pass a Bio::RangeI
           (e.g. Bio::Location::Simple or Bio::SegFeature::Generic)
           object to this method.

 Returns : set value or 0
 Args    : new value (optional)

  map
 Title   : map
 Usage   : $newpos = $obj->map(5);
 Function: Map the location from the input coordinate system
           to a new value in the output coordinate system.
 Example :
 Returns : new value in the output coordiante system
 Args    : a Bio::Location::Simple

  direction
 Title   : direction
 Usage   : $obj->direction('peptide');
 Function: Read-only method for the direction of mapping deduced from
           predefined input and output coordinate names.
 Example :
 Returns : 1 or -1, mapping direction
 Args    : new value (optional)

  swap
 Title   : swap
 Usage   : $obj->swap;
 Function: Swap the direction of transformation
           (input <-> output)
 Example :
 Returns : 1
 Args    :

  to_string
 Title   : to_string
 Usage   : $newpos = $obj->to_string(5);
 Function: Dump the internal mapper values into a human readable format
 Example :
 Returns : string
 Args    :

  _create_pair
 Title   : _create_pair
 Usage   : $mapper = $obj->_create_pair('chr', 'gene', 0, 2555, 10000, -1);
 Function: Internal helper method to create a mapper between
           two coordinate systems
 Returns : a Bio::Coordinate::Pair object
 Args    : string, input coordinate system name,
           string, output coordinate system name,
           boolean, strict mapping
           positive integer, offset
           positive integer, length
           1 || -1 , strand

  _translate
 Title   : _translate
 Usage   : $newpos = $obj->_translate($loc);
 Function: Translate the location from the CDS coordinate system
           to a new value in the propeptide coordinate system.
 Example :
 Returns : new location
 Args    : a Bio::Location::Simple or Bio::Location::SplitLocationI

  _reverse_translate
 Title   : _reverse_translate
 Usage   : $newpos = $obj->_reverse_translate(5);
 Function: Reverse translate the location from the propeptide
           coordinate system to a new value in the CSD.
           Note that a single peptide location expands to cover
           the codon triplet
 Example :
 Returns : new location in the CDS coordinate system
 Args    : a Bio::Location::Simple or Bio::Location::SplitLocationI

  _check_direction
 Title   : _check_direction
 Usage   : $obj->_check_direction();
 Function: Check and swap when needed the direction the location
           mapping Pairs based on input and output values
 Example :
 Returns : new location
 Args    : a Bio::Location::Simple

  _get_path
 Title   : _get_path
 Usage   : $obj->_get_path('peptide');
 Function: internal method for finding that shortest path between
           input and output coordinate systems.
           Calculations and caching are handled by the graph class.
           See L<Bio::Coordinate::Graph>.
 Example :
 Returns : array of the mappers
 Args    : none