Public Member Functions
public Bio::EnsEMBL::TranscriptMapper	new ()

protected Bio::EnsEMBL::Mapper	_load_mapper ()

public List	cdna2genomic ()

public List	genomic2cdna ()

public List	cds2genomic ()

public List	pep2genomic ()

public List	genomic2cds ()

public List	genomic2pep ()

Detailed Description

Synopsis

my $trmapper = Bio::EnsEMBL::TranscriptMapper->new($transcript);
 
@coords = $trmapper->cdna2genomic( 123, 554 );
 
@coords = $trmapper->genomic2cdna( 141, 500, -1 );
 
@coords = $trmapper->genomic2cds( 141, 500, -1 );
 
@coords = $trmapper->pep2genomic( 10, 60 );
 
@coords = $trmapper->genomic2pep( 123, 400, 1 );

Description

This is a utility class which can be used to perform coordinate conversions
between a number of coordinate systems relating to transcripts.

Any transcript object given to TranscriptMapper should have a proper Slice
object attached. The Slice provides vital information for the mapping process.
After TranscriptMapper has been instantiated, changes to the supplied 
Transcript will not affect the Mapper's results.

Definition at line 34 of file TranscriptMapper.pm.

Member Function Documentation

◆ _load_mapper()

protected Bio::EnsEMBL::Mapper Bio::EnsEMBL::TranscriptMapper::_load_mapper ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript for which a mapper should be created.
  Example    :

my $mapper = _load_mapper($transcript);

  Description: loads the mapper
  Returntype : Bio::EnsEMBL::Mapper
  Exceptions : none
  Caller     : Internal
  Status     : Stable

Code:

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sub _load_mapper {
  my $transcript = shift;
 
  my $mapper = Bio::EnsEMBL::Mapper->new( 'cdna', 'genomic');
 
  my $edits_on = $transcript->edits_enabled();
  my @edits;
 
  if($edits_on) {
    @edits = @{$transcript->get_all_SeqEdits()};
    @edits = sort {$a->start() <=> $b->start()} @edits;
  }
 
  my $edit_shift = 0;
 
  my $cdna_start = undef;
 
  my $cdna_end = 0;
 
 
  foreach my $ex (@{$transcript->get_all_Exons}) {
    my $gen_start = $ex->seq_region_start();
    my $gen_end   = $ex->seq_region_end();
 
    $cdna_start = $cdna_end + 1;
    $cdna_end   = $cdna_start + $ex->length() - 1;
 
    my $strand = $ex->strand();
 
    # add deletions and insertions into pairs when SeqEdits turned on
    # ignore mismatches (i.e. treat as matches)
    if($edits_on) {
      while(@edits && $edits[0]->start() + $edit_shift <= $cdna_end) {
 
        my $edit = shift(@edits);
        my $len_diff = $edit->length_diff();
 
        if($len_diff) {
          # break pair into two parts, finish first pair just before edit
 
          my $prev_cdna_end   = $edit->start() + $edit_shift - 1;
          my $prev_cdna_start = $cdna_start;
          my $prev_len        = $prev_cdna_end - $prev_cdna_start + 1;
 
          my $prev_gen_end;
          my $prev_gen_start;
          if($strand == 1) {
            $prev_gen_start = $gen_start;
            $prev_gen_end   = $gen_start + $prev_len - 1;
          } else {
            $prev_gen_start = $gen_end - $prev_len + 1;
            $prev_gen_end   = $gen_end;
          }
 
          if($prev_len > 0) { # only create map pair if not boundary case
            $mapper->add_map_coordinates
              ('cdna', $prev_cdna_start, $prev_cdna_end, $strand,
               'genome', $prev_gen_start,$prev_gen_end);
          }
 
          $cdna_start = $prev_cdna_end  + 1;
 
          if($strand == 1) {
            $gen_start  = $prev_gen_end + 1;
          } else {
            $gen_end    = $prev_gen_start - 1;
          }
 
          $cdna_end  += $len_diff;
 
          if($len_diff > 0) {
            $cdna_start += $len_diff;
          }
          else {
            if($strand == 1) {
              $gen_start  -= $len_diff;
            } else {
              $gen_end    += $len_diff;
            }
          }
 
          $edit_shift += $len_diff;
        }
      }
    }
 
    my $pair_len = $cdna_end - $cdna_start + 1;
 
    if($pair_len > 0) {
      $mapper->add_map_coordinates('cdna', $cdna_start, $cdna_end, $strand,
                                   'genome', $gen_start, $gen_end);
    }
  }
 
  return $mapper;
}

◆ cdna2genomic()

public List Bio::EnsEMBL::TranscriptMapper::cdna2genomic ( )

  Arg [1]    : $start
               The start position in cdna coordinates
  Arg [2]    : $end
               The end position in cdna coordinates
  Example    :

@cdna_coords = $transcript_mapper->cdna2genomic($start, $end);

  Description: Converts cdna coordinates to genomic coordinates.  The
               return value is a list of coordinates and gaps, where the coordinates
               are relative to the sequence region that the transcript used to construct
               this mapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throws if no start or end
  Caller     : general
  Status     : Stable

Code:

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◆ cds2genomic()

public List Bio::EnsEMBL::TranscriptMapper::cds2genomic ( )

  Arg [1]    : int $start
               start position in cds coords
  Arg [2]    : int $end
               end position in cds coords
  Arg [3]      boolean (0 or 1) $include_original_region
               option to include original input coordinate region mappings in the result
  Example    :

@genomic_coords = $transcript_mapper->cds2genomic(69, 306);

  Description: Converts cds coordinates into genomic coordinates. Coordinates returned
               are relative to sequence region that the transcript used to construct
               this mapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Gap and
               Bio::EnsEMBL::Mapper::Coordinate objects
  Exceptions : throws if no end
  Caller     : general
  Status     : at risk

Code:

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◆ genomic2cdna()

public List Bio::EnsEMBL::TranscriptMapper::genomic2cdna ( )

  Arg [1]    : $start
               The start position in genomic coordinates
  Arg [2]    : $end
               The end position in genomic coordinates
  Arg [3]    : $strand
               The strand of the genomic coordinates (default value 1)
  Example    :

@coords = $trans_mapper->genomic2cdna($start, $end, $strnd);

  Description: Converts genomic coordinates to cdna coordinates.  The
               return value is a list of coordinates and gaps.  Gaps
               represent intronic or upstream/downstream regions which do
               not comprise this transcripts cdna.  Coordinate objects
               represent genomic regions which map to exons (utrs included).
               Note: A poorly formed Transcript will cause this method to
               malfunction.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throws if start, end or strand not defined
  Caller     : general
  Status     : Stable

Code:

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◆ genomic2cds()

public List Bio::EnsEMBL::TranscriptMapper::genomic2cds ( )

  Arg [1]    : int $start
               The genomic start position
  Arg [2]    : int $end
               The genomic end position
  Arg [3]    : int $strand
               The genomic strand
  Example    :

@cds_coords = $trans_mapper->genomic2cds($start, $end, $strand);

  Description: Converts genomic coordinates into CDS coordinates of the
               transcript that was used to create this transcript mapper.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throw if start, end or strand not defined
  Caller     : general
  Status     : Stable

Code:

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sub genomic2cds {
 my ($self, $start, $end, $strand) = @_;
 
 if(!defined($start) || !defined($end) || !defined($strand)) {
   throw("start, end and strand arguments are required");
 }
 
 if($start > $end + 1) {
   throw("start arg must be less than or equal to end arg + 1");
 }
 
 my $cdna_cstart = $self->{'cdna_coding_start'};
 my $cdna_cend   = $self->{'cdna_coding_end'};
 
 #this is a pseudogene if there is no coding region
 if(!defined($cdna_cstart)) {
   #return a gap of the entire requested region, there is no CDS
   return Bio::EnsEMBL::Mapper::Gap->new($start,$end);
 }
 
 my @coords = $self->genomic2cdna($start, $end, $strand);
 
 my @out;
 
 foreach my $coord (@coords) {
   if($coord->isa('Bio::EnsEMBL::Mapper::Gap')) {
     push @out, $coord;
   } else {
     my $start = $coord->start;
     my $end   = $coord->end;
 
     if($coord->strand == -1 || $end < $cdna_cstart || $start > $cdna_cend) {
       #is all gap - does not map to peptide
       push @out, Bio::EnsEMBL::Mapper::Gap->new($start,$end);
     } else {
       #we know area is at least partially overlapping CDS
    
       my $cds_start = $start - $cdna_cstart + 1;
       my $cds_end   = $end   - $cdna_cstart + 1;
 
       if($start < $cdna_cstart) {
         #start of coordinates are in the 5prime UTR
         push @out, Bio::EnsEMBL::Mapper::Gap->new($start, $cdna_cstart-1);
 
         #start is now relative to start of CDS
         $cds_start = 1;
       }
    
       my $end_gap = undef;
       if($end > $cdna_cend) {
         #end of coordinates are in the 3prime UTR
         $end_gap = Bio::EnsEMBL::Mapper::Gap->new($cdna_cend + 1, $end);
         #adjust end to relative to CDS start
         $cds_end = $cdna_cend - $cdna_cstart + 1;
       }
 
       #start and end are now entirely in CDS and relative to CDS start
       $coord->start($cds_start);
       $coord->end($cds_end);
 
       push @out, $coord;
 
       if($end_gap) {
         #push out the region which was in the 3prime utr
         push @out, $end_gap;
       }
     }  
   }
 }
 
 return @out;
 
}

◆ genomic2pep()

public List Bio::EnsEMBL::TranscriptMapper::genomic2pep ( )

  Arg [1]    : $start
               The start position in genomic coordinates
  Arg [2]    : $end
               The end position in genomic coordinates
  Arg [3]    : $strand
               The strand of the genomic coordinates
  Example    :

@pep_coords = $transcript->genomic2pep($start, $end, $strand);

  Description: Converts genomic coordinates to peptide coordinates.  The
               return value is a list of coordinates and gaps.
  Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
               Bio::EnsEMBL::Mapper::Gap objects
  Exceptions : throw if start, end or strand not defined
  Caller     : general
  Status     : Stable

Code:

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◆ new()

public Bio::EnsEMBL::TranscriptMapper Bio::EnsEMBL::TranscriptMapper::new ( )

  Arg [1]    : Bio::EnsEMBL::Transcript $transcript
               The transcript for which a TranscriptMapper should be created.
  Example    :

$trans_mapper = Bio::EnsEMBL::TranscriptMapper->new($transcript)

  Description: Creates a TranscriptMapper object which can be used to perform
               various coordinate transformations relating to transcripts.
               Note that the TranscriptMapper uses the transcript state at the
               time of creation to perform the conversions, and that a new
               TranscriptMapper must be created if the Transcript is altered.
               'Genomic' coordinates are coordinates which are relative to the
               slice that the Transcript is on.
  Returntype : Bio::EnsEMBL::TranscriptMapper
  Exceptions : throws if a transcript is not an argument
  Caller     : Transcript::get_TranscriptMapper
  Status     : Stable

Code:

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◆ pep2genomic()

public List Bio::EnsEMBL::TranscriptMapper::pep2genomic ( )

  Arg [1]    : int $start
               start position in peptide coords
  Arg [2]    : int $end
               end position in peptide coords
  Example    :

@genomic_coords = $transcript_mapper->pep2genomic(23, 102);

  Description: Converts peptide coordinates into genomic coordinates.  The
               coordinates returned are relative to the sequence region that the
               transcript used to construct this TranscriptMapper was on.
  Returntype : list of Bio::EnsEMBL::Mapper::Gap and
               Bio::EnsEMBL::Mapper::Coordinate objects
  Exceptions : throws if no end
  Caller     : general
  Status     : Stable

Code:

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The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/TranscriptMapper.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _load_mapper()

◆ cdna2genomic()

◆ cds2genomic()

◆ genomic2cdna()

◆ genomic2cds()

◆ genomic2pep()

◆ new()

◆ pep2genomic()