only_proteing_coding filter added to SliceAdaptor::fetch_all
Created by: vsitnik
optimization for SliceAdaptor::fetch_all to get only regions, that have 'coding_cnt' attribute > 0. used to speed up the whole proteome download for vb_proteome_download projects.
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Description
optimization for SliceAdaptor::fetch_all to get only regions, that have 'coding_cnt' attribute > 0. used to speed up the whole proteome download for vb_proteome_download projects.
Use case
used to speed up the whole proteome download for vb_proteome_download projects. i.e. in the sequence/proteome/:species rest-api endpoint:
my ($toplevel, $ver, $non_ref, $dup, $lrg, $only_protein_coding) = ('toplevel', undef, undef, undef, undef, 1);
my $slices = $adaptor->fetch_all($toplevel, $ver, $non_ref, $dup, $lrg, $only_protein_coding);
Catalyst::Exception->throw("No slice found for the toplevel coord system") unless $slices;
Benefits
will speed up the whole proteome downloads for genomes, having large number contigs without any genes or without protein coding ones (i.e. partly assembled genomes)
Possible Drawbacks
The 'coding_cnt' attribute should be set for the 'seq_region_atrrib' for the filter to work.
Testing
test are added to t/sliceAdaptor.t tests are ok. no regression. 'All tests successful. Result: PASS'