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Pubchem #255

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a407e01
Add extrarealationship for merge alleles with a point mutation of the…
ianlongden Feb 28, 2025
0b20f15
Add feature with same name to highlight BUG
ianlongden Mar 2, 2025
0d1b19d
more chems needed
ianlongden Apr 22, 2025
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2 changes: 1 addition & 1 deletion Load/chemical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ def add_chemical_data(cursor, cvterm_id, organism_id, dbxref_id, pub_id, db_id,
pubchem_pub_id = cursor.fetchone()[0]

obsolete = False
for i in range(20):
for i in range(30):
cursor.execute(dbxref_sql, (db_id['CHEBI'], f"{i+1}"))
chem_dbxref_id = cursor.fetchone()[0]
##################################################################################
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31 changes: 28 additions & 3 deletions Load/gene_alleles.py
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Original file line number Diff line number Diff line change
Expand Up @@ -191,7 +191,22 @@ def feature_relationship_add(cursor, count, feat_details, tool_name, gene_name,
if 'org_abbr' in feat_details:
org_id = org_dict[feat_details['org_abbr']]
uniquename = feat_details['uniquename'].replace('<number>', "{:07d}".format(allele_count))
if name not in feature_id:
uniquename = uniquename.replace('<allele_name>', allele_name)
print(f"NOTICE: processing {name} {uniquename}")
if name == uniquename:
cursor.execute(dbxref_sql, (db_id['FlyBase'], uniquename))
dbxref_id = cursor.fetchone()[0]
cursor.execute(feat_sql, (dbxref_id, org_id, name, uniquename,
"", 0, cvterm_id[feat_details['type']]))
feat2_id = cursor.fetchone()[0]

# add synonyms
cursor.execute(syn_sql, (name, cvterm_id['symbol'], name))
symbol_id = cursor.fetchone()[0]

# add feature_synonym
cursor.execute(fs_sql, (symbol_id, feat2_id, pub_id, True))
elif name not in feature_id:
# create dbxref, accession -> uniquename
cursor.execute(dbxref_sql, (db_id['FlyBase'], uniquename))
dbxref_id = cursor.fetchone()[0]
Expand Down Expand Up @@ -374,13 +389,15 @@ def add_relationships(rela_list, cursor, count, tool_name, gene_name, allele_nam
mess = feature_relationship_add(cursor, count, item, tool_name, gene_name, allele_name, feat1_id,
cvterm_id, org_id, db_id, rela_pub, feature_id, org_dict)
log += " {}".format(mess)

return log


def create_gene_alleles(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id,
num_genes=5, num_alleles=3, gene_prefix=None, allele_prefix=None,
tool_prefix=None, gene_relationships=None, allele_relationships=None, pub_format=None,
gene_props=None, allele_props=None, org_abbr='Dmel', allele_org_abbr='Dmel'
gene_props=None, allele_props=None, org_abbr='Dmel', allele_org_abbr='Dmel',
add_same_name=False
):
"""Create the genes and alleles.

Expand Down Expand Up @@ -411,6 +428,8 @@ def create_gene_alleles(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id,
alelele_props: <dict>props to be added to each allele. dict has a field: [proptype, value] format
org_abbr: <string> (default 'Dmel') abbreviation for the organism.
allele_org_abbr: <string> (default 'Dmel') abbreviation for the alleles organism.
add_same_name: <bool> Some tests require an allele relationship of the same name.
See PDEV-PDEV-251
Return List: List of genes and their alleles.
[gene_id1, [allele_id1, allele_id2],
gene_id2, [allele_id3, allele_id4]]
Expand All @@ -430,6 +449,11 @@ def create_gene_alleles(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id,
'uniquename': 'FBto<number>',
'type': 'engineered_region',
'relationship': 'associated_with'})
if add_same_name:
allele_relationships.append({'name': "<allele_name>",
'uniquename': '<allele_name>',
'type': 'point_mutation',
'relationship': 'partof'})
gene_allele_list = []
for i in range(num_genes):
if pub_format:
Expand Down Expand Up @@ -632,7 +656,8 @@ def create_merge_allele(cursor, org_dict, feature_id, cvterm_id, db_id, pub_id):
allele_prefix=None,
tool_prefix='Clk',
allele_relationships=allele_relationships,
pub_format="merge_title_"
pub_format="merge_title_",
add_same_name=True
)
for g_a in gene_alleles:
print("gene {}".format(g_a[0]))
Expand Down