[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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