Bio::Coordinate::GeneMapper - transformations between gene related coordinate systems 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); 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.

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/ Email: heikki@ebi.ac.uk Address: EMBL Outstation, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambs. CB10 1SD, United Kingdom 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