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Commit 99ff8cb8 authored by Ian Longden's avatar Ian Longden
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new faster sql

parent 5ef55fec
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Showing with 38 additions and 12 deletions
misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm
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...@@ -1293,18 +1293,44 @@ SQL ...@@ -1293,18 +1293,44 @@ SQL
####################################################################### #######################################################################
my $gene_desc_sql =(<<DXS); my $gene_desc_sql =(<<DXS);
SELECT gtt.gene_id, x.description, s.source_id, x.accession select IF (ox.ensembl_object_type = 'Gene', gtt_gene.gene_id,
FROM source s, xref x, object_xref ox, identity_xref ix, gene_transcript_translation gtt, gene_desc_prioritys p IF (ox.ensembl_object_type = 'Transcript', gtt_transcript.gene_id,
WHERE x.source_id = s.source_id gtt_translation.gene_id)) AS gene_id,
AND s.source_id = p.source_id x.description AS description,
AND x.xref_id = ox.xref_id s.source_id AS source_id,
AND ox.ox_status = "DUMP_OUT" x.accession AS accession
AND ( (ox.ensembl_object_type = "Transcript" and gtt.transcript_id = ox.ensembl_id) from ( gene_desc_prioritys p
OR (ox.ensembl_object_type = "Translation" and gtt.translation_id = ox.ensembl_id) join ( source s
OR (ox.ensembl_object_type = "Gene" and gtt.gene_id = ox.ensembl_id) join ( xref x
) join ( object_xref ox
AND ox.object_xref_id = ix.object_xref_id join ( identity_xref ix
ORDER BY gtt.gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC ) using (object_xref_id)
) using (xref_id)
) using (source_id)
) using (source_id)
)
left join gene_transcript_translation gtt_gene
on (gtt_gene.gene_id = ox.ensembl_id)
left join gene_transcript_translation gtt_transcript
on (gtt_transcript.transcript_id = ox.ensembl_id)
left join gene_transcript_translation gtt_translation
on (gtt_translation.translation_id = ox.ensembl_id)
where ox.ox_status = 'DUMP_OUT'
order by gene_id desc,
p.priority desc,
(ix.target_identity+ix.query_identity) desc
# SELECT gtt.gene_id, x.description, s.source_id, x.accession
# FROM source s, xref x, object_xref ox, identity_xref ix, gene_transcript_translation gtt, gene_desc_prioritys p
# WHERE x.source_id = s.source_id
# AND s.source_id = p.source_id
# AND x.xref_id = ox.xref_id
# AND ox.ox_status = "DUMP_OUT"
# AND ( (ox.ensembl_object_type = "Transcript" and gtt.transcript_id = ox.ensembl_id)
# OR (ox.ensembl_object_type = "Translation" and gtt.translation_id = ox.ensembl_id)
# OR (ox.ensembl_object_type = "Gene" and gtt.gene_id = ox.ensembl_id)
# )
# AND ox.object_xref_id = ix.object_xref_id
# ORDER BY gtt.gene_id DESC, p.priority DESC, (ix.target_identity+ix.query_identity) DESC
DXS DXS
######################################################################## ########################################################################
......
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