Mercurial > repos > greg > plant_tribes_gene_family_scaffold_loader
changeset 5:cb986be6355e draft
Uploaded
| author | greg |
|---|---|
| date | Tue, 05 Jun 2018 10:56:33 -0400 |
| parents | 3c6514d810ae |
| children | 9a4b0ae3d408 |
| files | gene_family_scaffold_loader.py |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/gene_family_scaffold_loader.py Fri May 25 10:46:18 2018 -0400 +++ b/gene_family_scaffold_loader.py Tue Jun 05 10:56:33 2018 -0400 @@ -350,7 +350,7 @@ sql = "SELECT id FROM plant_tribes_taxon WHERE species_name = '%s';" % species_name cur = self.conn.cursor() cur.execute(sql) - taxon_id = cur.fetchone()[0] + taxon_id_db = cur.fetchone()[0] # If the plant_tribes_gene table contains a row that has the gene_id, # then we'll add a row only to the gene_scaffold_orthogroup_association table. sql = "SELECT id FROM plant_tribes_gene WHERE gene_id = '%s';" % gene_id @@ -360,10 +360,10 @@ gene_id_db = cur.fetchone()[0] except: # Insert a row into the plant_tribes_gene table. - args = [gene_id, taxon_id, dna_sequence, aa_sequence] + args = [gene_id, dna_sequence, aa_sequence] sql = """ INSERT INTO plant_tribes_gene - VALUES (nextval('plant_tribes_gene_id_seq'), %s, %s, %s, %s) + VALUES (nextval('plant_tribes_gene_id_seq'), %s, %s, %s) RETURNING id; """ cur = self.update(sql, tuple(args)) @@ -378,10 +378,10 @@ for scaffold_rec in self.scaffold_recs: if scaffold_id in scaffold_rec and clustering_method in scaffold_rec: scaffold_id_db = scaffold_rec[0] - args = [gene_id_db, scaffold_id_db, orthogroup_id_db] + args = [gene_id_db, scaffold_id_db, orthogroup_id_db, taxon_id_db] sql = """ - INSERT INTO gene_scaffold_orthogroup_association - VALUES (nextval('gene_scaffold_orthogroup_association_id_seq'), %s, %s, %s); + INSERT INTO gene_scaffold_orthogroup_taxon_association + VALUES (nextval('gene_scaffold_orthogroup_taxon_association_id_seq'), %s, %s, %s, %s); """ cur = self.update(sql, tuple(args)) self.flush()