[ensembl-dev] how to use the transcript mapper

Andrea Edwards edwardsa at cs.man.ac.uk
Mon Nov 1 13:46:36 GMT 2010


Hi

I'm a bit confused by the transcript mapper. The docs say about the 
cdna2genomic method

   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.
   Returntype : list of Bio::EnsEMBL::Mapper::Coordinate and
                Bio::EnsEMBL::Mapper::Gap objects
   Exceptions : throws if no start or end
   Caller     : general
   Status     : Stable



What would/could the gaps be in a transcript?

If your transcript did contain gaps would the return value be an array 
which contained both refs to coordinate objects and gap objects and you 
would have to iterate over the array and determine the type of the ref 
at each position?

thanks
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