changes needed for expression tests

Load/drivers.py

@@ -11,13 +11,19 @@ def add_driver_data(cursor, org_dict, feature_id, cvterm_id, dbxref_id, pub_id,
     fs_sql = """ INSERT INTO feature_synonym (synonym_id, feature_id,  pub_id) VALUES (%s, %s, %s) """
     feat_rel_sql = """ INSERT INTO feature_relationship (subject_id, object_id,  type_id) VALUES (%s, %s, %s) RETURNING feature_relationship_id """
 
-    count = gene_count = 400000
+    # create domain
+    dom_name = 'DBD'
+    cursor.execute(feat_sql, (None, org_dict['Dmel'], 'DBD and LBD domains', 'ss-XP_DBD and LBD domains',
+                              "", 0, cvterm_id['polypeptide']))
+    feature_id[dom_name] = cursor.fetchone()[0]
+
+    count = gene_count = 500000
     for start in ['Scer\\GAL4', 'Hsap\\RELA']:
         # create gene
-        gene_count += 1
         org_id = org_dict[start[:4]]
         sym_name = "{}".format(start)
-        unique_name = 'FBgn:{:07d}'.format(gene_count)
+        count = count + 1
+        unique_name = 'FBgn{:07d}'.format(count)
         print("Adding gene {} {} for species {} - syn {}".format(unique_name, gene_count, start[:4], sym_name))
         # create dbxref,  accession -> uniquename
         cursor.execute(dbxref_sql, (db_id['FlyBase'], unique_name))
@@ -28,23 +34,59 @@ def add_driver_data(cursor, org_dict, feature_id, cvterm_id, dbxref_id, pub_id,
         feature_id[sym_name] = gene_id = cursor.fetchone()[0]
 
         for i in range(10):
-            # create allele/driver.
+            # select f.name, cvt2.name, f.uniquename, o.abbreviation, cvt.name
+            # from feature_relationship fr, cvterm cvt2, cvterm cvt,  feature f, organism o
+            # where f.type_id = cvt2.cvterm_id and fr.object_id = f.feature_id and fr.type_id = cvt.cvterm_id and
+            #       o.organism_id = f.organism_id and subject_id = 23124422;
+            #        name       |              name               | uniquename  | abbreviation |           name
+            # ------------------+---------------------------------+-------------+--------------+---------------------------
+            #  Scer\GAL4        | gene                            | FBgn0014445 | Scer         | alleleof
+            #  P{GAL4(DBD)-hb}  | transgenic_transposable_element | FBtp0001259 | Ssss         | associated_with
+            #  pP{GAL4(DBD)-hb} | engineered_plasmid              | FBmc0001249 | Ssss         | gets_expression_data_from
+            #  hb               | gene                            | FBgn0001180 | Dmel         | has_reg_region
+            if start == 'Scer\\GAL4':
+                gene_name = f'hb{i+1}'
+            else:
+                gene_name = f'pxn{i + 1}'
             count = count + 1
-            al_sym_name = "{}[{}]".format(start, count)
-            unique_name = 'FBal:{:07d}'.format(count)
-            # create dbxref,  accession -> uniquename
-            print("Adding allele {} {} for species {} - syn {}".format(unique_name, count, start[:4], sym_name))
+            al_sym_name = "{}<up>{}.{}</up>".format(start, dom_name, gene_name)
+            al_name = "{}[{}.{}]".format(start, dom_name, gene_name)
+            unique_name = 'FBal{:07d}'.format(count)
+            print("Adding allele {} {} for species {} - syn {}".format(unique_name, count, start[:4], al_name))
             cursor.execute(dbxref_sql, (db_id['FlyBase'], unique_name))
             al_dbxref_id = cursor.fetchone()[0]
 
-            cursor.execute(feat_sql, (al_dbxref_id, org_id, al_sym_name, count, None, 0, cvterm_id['gene']))
-            feature_id[al_sym_name] = allele_id = cursor.fetchone()[0]
+            cursor.execute(feat_sql, (al_dbxref_id, org_id, al_name, unique_name, None, 0, cvterm_id['allele']))
+            feature_id[al_name] = cursor.fetchone()[0]
+            # add synonyms
+            cursor.execute(syn_sql, (feature_id[al_name], cvterm_id['symbol'], al_sym_name))
+            syn_id = cursor.fetchone()[0]
+            cursor.execute(fs_sql, (syn_id, feature_id[al_name], pub_id))
+
+            cursor.execute(syn_sql, (feature_id[al_name], cvterm_id['symbol'], al_sym_name[5:]))  # skip sp name
+            syn_id = cursor.fetchone()[0]
+            cursor.execute(fs_sql, (syn_id, feature_id[al_name], pub_id))
+            #  Scer\GAL4        | gene                            | FBgn0014445 | Scer         | alleleof
+            cursor.execute(feat_rel_sql, (feature_id[al_name], feature_id[start], cvterm_id['alleleof']))
+
+            #  hb               | gene                            | FBgn0001180 | Dmel         | has_reg_region
+            unique_name = 'FBgn{:07d}'.format(count)
+            print("Adding gene {} for species {} - syn {}".format(unique_name, start[:4], gene_name))
+            cursor.execute(dbxref_sql, (db_id['FlyBase'], unique_name))
+            gene_dbxref_id = cursor.fetchone()[0]
+            cursor.execute(feat_sql, (gene_dbxref_id, org_id, gene_name, unique_name, None, 0, cvterm_id['gene']))
+            feature_id[gene_name] = cursor.fetchone()[0]
+            # add synonym
+            # select * from synonym where synonym_id = 6922299;
+            # synonym_id | name | type_id | synonym_sgml
+            # ------------+-------------------+---------+--------------------------
+            # 6922299 | Hsap\RELA[AD.Pxn] | 59978 | Hsap\RELA<up>AD.Pxn</up>
+            cursor.execute(syn_sql, (feature_id[gene_name], cvterm_id['symbol'], gene_name))
+            syn_id = cursor.fetchone()[0]
+            cursor.execute(fs_sql, (syn_id, feature_id[gene_name], pub_id))
+
+            cursor.execute(feat_rel_sql, (feature_id[al_name], feature_id[gene_name], cvterm_id['has_reg_region']))
 
-            # add as feature relationship
-            cursor.execute(feat_rel_sql, (allele_id, gene_id, cvterm_id['alleleof']))
+            #  P{GAL4(DBD)-hb}  | transgenic_transposable_element | FBtp0001259 | Ssss         | associated_with
 
-            # add synonym for allele
-            cursor.execute(syn_sql, (al_sym_name, cvterm_id['symbol'], al_sym_name))
-            symbol_id = cursor.fetchone()[0]
-            # add feature_synonym for allele
-            cursor.execute(fs_sql, (symbol_id, allele_id, pub_id))
+            #  pP{GAL4(DBD)-hb} | engineered_plasmid              | FBmc0001249 | Ssss         | gets_expression_data_from

add-test_data.py

@@ -21,6 +21,7 @@
 from Load.grp import add_grp_data
 from Load.cell_line import add_cell_line_data
 from Load.aberration import add_aberration_data
+from Load.drivers import add_driver_data
 
 conn = psycopg2.connect(database="fb_test")
 cursor = conn.cursor()
@@ -522,6 +523,8 @@ def load_pub_author_pubprop(parsed_yaml):
 # Disease Implicated Variants (DIV)
 add_div_data(cursor, organism_id, cv_cvterm_id, feature_id, pub_id, db_dbxref)
 
+# add drivers
+add_driver_data(cursor, organism_id, feature_id, cvterm_id, dbxref_id, pub_id, db_id)
 
 # add chromosome_structure_variation
 print("Adding chromosome_structure_variation data.")

data/cv_cvterm.yaml

@@ -8,10 +8,13 @@ SO: ['chromosome_arm', 'chromosome', 'gene', 'mRNA', 'DNA', 'golden_path', 'ncRN
      'natural population', 'cloned_region', 'engineered_region', 'transgenic_transposable_element',
      'transposable_element_insertion_site', 'chromosome_band', 'allele', 'transposable_element',
      'natural_transposable_element', 'gene_group', 'polypeptide', 'chromosome_breakpoint', 'engineered_plasmid', 'sgRNA',
-     'oligo', 'engineered_foreign_gene', 'point_mutation', 'cDNA_clone', 'TSS', 'rescue_region', 'insertion_site']
+     'oligo', 'engineered_foreign_gene', 'point_mutation', 'cDNA_clone', 'TSS', 'rescue_region', 'insertion_site', 'synthetic_sequence']
 molecular_function: ['mRNA binding']
-cellular_component: ['nucleolus', 'something' ,'extracellular space']
+cellular_component: ['nucleolus', 'something' ,'extracellular space', 'endoplasmic reticulum']
 biological_process: ['activation of immune response', 'defense response to other organism', 'rRNA processing']
+FlyBase anatomy CV: ['embryo','dopaminergic PAM neuron 1', 'dopaminergic PAM neuron 5', 'dissociated larval fat cell',
+                     'embryonic/larval hemolymph',
+                     'anatomy 1', 'anatomy 2', 'anatomy 3', 'mesoderm']
 ####### End of order matters cv/cvterms
 
 cell_line_cvtermprop type: ['basis']
@@ -24,8 +27,8 @@ CHEBI: []
 DOID: []
 disease_ontology: ['hh-1']
 
-experimental assays: ['distribution deduced from reporter (Gal4 UAS)']
-expression slots: ['stage', 'anatomy', 'assay']
+experimental assays: ['distribution deduced from reporter (Gal4 UAS)', 'in situ']
+expression slots: ['stage', 'anatomy', 'assay', 'cellular']
 
 feature_cvtermprop type: [
     'wt_class', 'aberr_class', 'tool_uses', 'transgene_uses property',
@@ -36,9 +39,7 @@ feature_relationshipprop type: ['fly_disease-implication_change', 'comment', 're
 
 FlyBase: ['FlyBase analysis']
 FlyBase_internal: ['pubprop type:curated_by']
-FlyBase anatomy CV: ['embryo','dopaminergic PAM neuron 1', 'dopaminergic PAM neuron 5',
-                     'embryonic/larval hemolymph',
-                     'anatomy 1', 'anatomy 2', 'anatomy 3']
+
 FlyBase development CV: ['late embryonic stage', 'embryonic stage', 'adult stage', 'development 1', 'development 2', 'development 3',
                          'wandering third instar larval stage']
 FlyBase miscellaneous CV: [
@@ -52,6 +53,7 @@ FlyBase miscellaneous CV: [
     'pheno1', 'pheno2', 'pheno3', 'pheno4', 'pheno5',
     'photoactivatable fluorescent protein', 'protein detection tool', 'project',
     'qualifier', 'reagent collection', 'RNA detection tool', 'single balancer', 'spontaneous',
+    'split system combination',
     'transcriptome', 'umbrella project', 'unspecified']
 
 GenBank feature qualifier: [
@@ -83,7 +85,7 @@ property type: [
     'GO_internal_notes', 'GO_review_date', 'HDM_comment', 'OMIM_pheno_table', 'PCR_template',
     'aberr_relationships',
     'additional_disease-implication_change', 'allele_report_comment',
-    'aminoacid_rep', 'availability','balancer_status', 'bodypart_expression_marker', 'bound_moiety_comment', 'breeding_comment', 'category', 'cellular_description',
+    'aminoacid_rep', 'availability','balancer_status', 'bodypart_expression_text', 'bodypart_expression_marker', 'bound_moiety_comment', 'breeding_comment', 'category', 'cellular_description',
     'comment', 'complementation', 'cyto_change_comment', 'cyto_loc_comment', 'curated_phenotype', 'data_analysis', 'data_type', 'data_link', 'data_link_bdsc', 'deliberate_omission',
     'deleted_segment', 
     'derived_cyto_location', 'description', 'diopt_ortholog', 'discoverer', 'disease_associated', 'div_comment',
@@ -131,7 +133,7 @@ relationship type: [
     'identified_with', 'maps_to_clone', 'member_gene_of', 'molec_deletes', 'molec_dups',
     'molec_nondeletes', 'molec_nondups', 'molec_partdeletes', 'molec_partdups', 
     'nomaps_to_clone', 'nondeletes', 'nonduplicates', 'originates_from',
-    'overlap_inferred', 'parent_grp', 'part_deletes', 'part_duplicates', 'partof',
+    'overlap_inferred', 'partially_produced_by', 'parent_grp', 'part_deletes', 'part_duplicates', 'partof',
     'primer_progenitor_of', 'producedby', 'progenitor', 'replacement_descendant_of', 'representative_isoform',
     'recom_right_end', 'recom_left_end', 'related_tool', 'segregant_of', 'tagged_with', 'undefined_grp']
 

triggers/multiple_seqs.sql

@@ -16,7 +16,7 @@ $bob$
 LANGUAGE plpgsql;
 
 SELECT make_fb_seqs(ARRAY['al', 'ti', 'tp', 'te', 'mc', 'ms', 'ba', 'ab', 'gn', 'tr', 'pp', 'og',
-                          'cl', 'gg', 'hh', 'ig', 'lc', 'rf', 'sf', 'sn', 'st', 'tc', 'to', 'ch']);
+                          'cl', 'gg', 'hh', 'ig', 'lc', 'rf', 'sf', 'sn', 'st', 'tc', 'to', 'ch', 'co']);
 
 CREATE OR REPLACE FUNCTION public.feature_assignname_fn_i()
  RETURNS trigger