Merge pull request #204 from VirtualFlyBrain/xrefs

increase output of get_transcriptomic_profile
VirtualFlyBrain · Sep 4, 2024 · 8680100 · 8680100
2 parents 6242b3a + d78f7ac
commit 8680100
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/src/vfb_connect/cross_server_tools.py b/src/vfb_connect/cross_server_tools.py
@@ -699,10 +699,16 @@ def get_transcriptomic_profile(self, cell_type, gene_type=False, no_subtypes=Fal
                  "OPTIONAL MATCH (sa)-[:overlaps]->(tis:Class:Anatomy) "
                  "OPTIONAL MATCH (clus)-[:has_source]->(ds:DataSet:Individual) "
                  "OPTIONAL MATCH (ds)-[:has_reference]->(p:pub:Individual) "
-                 "OPTIONAL MATCH (ds)-[dbx:database_cross_reference]->(s:Site:Individual) "
+                 "OPTIONAL MATCH (ds)-[dbxw:database_cross_reference]->(sw:Site:Individual "
+                 "{short_form:'scExpressionAtlas'}) "
+                 "OPTIONAL MATCH (ds)-[dbxd:database_cross_reference]->(sd:Site:Individual "
+                 "{short_form:'scExpressionAtlasFTP'}) "
                  "RETURN DISTINCT c2.label AS cell_type, c2.short_form AS cell_type_id, "
                  "sex.label AS sample_sex, COLLECT(tis.label) AS sample_tissue, "
-                 "p.miniref[0] as ref, g.label AS gene, g.short_form AS gene_id, "
+                 "ds.short_form AS dataset_id, p.miniref[0] as ref, "
+                 "COLLECT(DISTINCT sw.link_base[0] + dbxw.accession[0]) AS website_linkouts, "
+                 "sd.link_base[0] + dbxd.accession[0] + sd.postfix[0] AS download_linkout, "
+                 "g.label AS gene, g.short_form AS gene_id, "
                  "apoc.coll.subtract(labels(g), ['Class', 'Entity', 'hasScRNAseq', 'Feature', 'Gene']) AS function, "
                  "e.expression_extent[0] as extent, toFloat(e.expression_level[0]) as level "
                  "ORDER BY cell_type, g.label" % (gene_label, cell_type_short_form, equal_condition))