Merge pull request #125 from GavinHuttley/develop

ENH: extend gene data available for querying

src/ensembl_lite/_genomedb.py

@@ -185,6 +185,8 @@ class EnsemblGffDb(SqliteDbMixin):
  "score": "TEXT", # check defn
  "strand": "TEXT",
  "phase": "TEXT",
+ "symbol": "TEXT",
+ "description": "TEXT",
  "attributes": "TEXT",
  "comments": "TEXT",
  "spans": "array", # aggregation of coords across records
@@ -205,6 +207,7 @@ class EnsemblGffDb(SqliteDbMixin):
  "stop",
  "is_canonical",
  "biotype_id",
+ "symbol",
  ),
  "related_feature": ("gene_id", "related_id"),
  }
@@ -240,7 +243,9 @@ def _create_views(self) -> None:
  f.spans as spans,
  f.stableid as name,
  f.is_canonical as is_canonical,
- f.id as feature_id
+ f.id as feature_id,
+ f.symbol as symbol,
+ f.description as description
  FROM feature f
  JOIN biotype b ON f.biotype_id = b.id
  """

src/ensembl_lite/data/sample.cfg

@@ -7,8 +7,8 @@ path=pub
 # and where the installation will be placed.
 # The paths can be absolute (begin with /), as in this case,
 # or relative to the location of this cfg file (begin with ./).
-staging_path=/tmp/ensembldb_download
-install_path=/tmp/ensembldb
+staging_path=ensembl_download_112
+install_path=ensembl_install_112
 [release]
 # The release of Ensembl that you want to sample data from.
 release=112