remove sql usage of assembly_exception table

refs #25
refs #22

As of ensembl 110, this table was emptied causing our detection of
primary assembly to be flawed. This adopts a slightly flawed approach
for detecting the primary assembly, but one that should unblock
builds. Chromosomes detection is also now incomplete.

ensembl_genes/notebooks/ensembl_genes_eda.ipynb

@@ -43,7 +43,7 @@
    "source": [
     "# parameters cell\n",
     "species = \"human\"\n",
-    "release = \"104\""
+    "release = \"111\""
    ]
   },
   {
@@ -154,7 +154,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "ensg.gene_df.seq_region_exc_type.value_counts(dropna=False)"
+    "pd.crosstab(ensg.gene_df.coord_system, ensg.gene_df.primary_assembly, margins=True)"
    ]
   },
   {
@@ -597,7 +597,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.10.12"
   }
  },
  "nbformat": 4,

ensembl_genes/queries/gene_alt_alleles.sql

@@ -1,8 +1,13 @@
+-- Get alt allele groups: genes with multiple alleles
 SELECT
   gene.stable_id AS ensembl_gene_id,
   alt_allele.alt_allele_group_id,
   alt_allele_attrib.attrib = "IS_REPRESENTATIVE" AS alt_allele_is_representative,
-  assembly_exception.exc_seq_region_id IS NULL AS primary_assembly,
+  -- we used to use assembly_exception to determine primary assembly, but this table is now empty
+  -- https://github.com/related-sciences/ensembl-genes/issues/22#issuecomment-1664197773
+  -- instead just look for a short seq_region name (e.g. '19' instead of 'HSCHR19LRC_PGF1_CTG3_1'),
+  -- even though this is a flawed method that would miss scaffolds that are primary assemblies.
+  LENGTH(seq_region.name) <= 3 AS primary_assembly,
   seq_region.name AS seq_region,
   alt_allele_attrib.attrib AS alt_allele_attrib,
   gene.created_date AS ensembl_created_date
@@ -13,11 +18,6 @@ INNER JOIN alt_allele_attrib
   ON alt_allele.alt_allele_id = alt_allele_attrib.alt_allele_id
 INNER JOIN seq_region
   ON gene.seq_region_id = seq_region.seq_region_id
-LEFT JOIN assembly_exception
-  ON seq_region.seq_region_id = assembly_exception.seq_region_id
-  -- keep exc_type in (PATCH_FIX, PATCH_NOVEL, HAP)
-  -- refs internal Related Sciences issue 606.
-  AND NOT assembly_exception.exc_type <=> "PAR"
 -- all genes were current when query was written, ensure this is always the case
 WHERE gene.is_current
 ORDER BY alt_allele_group_id, alt_allele_is_representative DESC, primary_assembly DESC, ensembl_created_date, ensembl_gene_id

ensembl_genes/queries/genes.sql

@@ -15,26 +15,24 @@ SELECT
   gene.modified_date AS ensembl_modified_date,
   coord_system.version AS coord_system_version,
   coord_system.name AS coord_system,
-  -- get chromosome: refs internal Related Sciences issue 606.
-  CASE WHEN coord_system.name = "chromosome"
-       THEN COALESCE(exc_seq_region.name, seq_region.name)
+  -- we are not able to determine the chromosomes not on the primary assembly
+  CASE WHEN LENGTH(seq_region.name) <= 3
+       THEN seq_region.name
        END AS chromosome,
-  assembly_exception.exc_type AS seq_region_exc_type,
   seq_region.name AS seq_region,
   gene.seq_region_start AS seq_region_start,
   gene.seq_region_end AS seq_region_end,
   gene.seq_region_strand AS seq_region_strand,
-  assembly_exception.exc_seq_region_id IS NULL AS primary_assembly
+  -- we used to use assembly_exception to determine primary assembly, but this table is now empty
+  -- https://github.com/related-sciences/ensembl-genes/issues/22#issuecomment-1664197773
+  -- instead just look for a short seq_region name (e.g. '19' instead of 'HSCHR19LRC_PGF1_CTG3_1')
+  -- even though this is a flawed method that would miss scaffolds that are primary assemblies.
+  LENGTH(seq_region.name) <= 3 AS primary_assembly
 FROM gene
 LEFT JOIN xref ON xref.xref_id = gene.display_xref_id
 LEFT JOIN external_db ON xref.external_db_id = external_db.external_db_id
 LEFT JOIN seq_region ON gene.seq_region_id = seq_region.seq_region_id
 LEFT JOIN coord_system ON seq_region.coord_system_id = coord_system.coord_system_id
-LEFT JOIN assembly_exception ON seq_region.seq_region_id = assembly_exception.seq_region_id
-  -- keep exc_type in (PATCH_FIX, PATCH_NOVEL, HAP)
-  -- refs internal Related Sciences issue 606.
-  AND NOT assembly_exception.exc_type <=> "PAR"
-LEFT JOIN seq_region AS exc_seq_region ON assembly_exception.exc_seq_region_id = exc_seq_region.seq_region_id
 WHERE
   -- all genes were current when query was written, ensure this is always the case
   gene.is_current AND