[Bioperl-pipeline] Genewise matters(start,stop modification)

[Bala]

Hi Elia,


>
> No, meaning that when you are finished buildign the genes, and you wan tto
> store them you can't store them as they are because you have passed ina
> piece of the contig (start,end,strand) so you n eed to convert the
> coordinates to the original ones before stroing it.

I have an idea, to solve the above issue...(hope its not a hack)

In the Genewise wrapper right,

In the  _run subroutine ,

my $gene = $genewiseParser->next_prediction($filehandle);

Hence once we get the $gene object,

We add the original start stop of the genomic and protein to
the current start stop of the gene,exon and the
supporting features(in this sub routine itself or another internal function
eg  _modify_genes(@genes)).

genomic_new start = the current start + $self->_subject_dna_seq->start
genomic_new end  = the current start +$self->_subject_dna_seq->end

protein_new_start= the current start + $self->_query_pep_seq->start
protein_new end   = the current start + $self->_query_pep_seq->end

and then return the modified genes.

please comment


Thank you

Bala