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biology
chemistry
drug-discovery
clinical-trials
protein-protein-interaction
gene-essentiality
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6d1bbc7 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 | """Tests for PPI protein mapper: UniProt validation & canonical pair ordering."""
from pathlib import Path
import pytest
from negbiodb_ppi.ppi_db import get_connection, run_ppi_migrations
from negbiodb_ppi.protein_mapper import (
canonical_pair,
get_or_insert_protein,
validate_uniprot,
)
MIGRATIONS_DIR = Path(__file__).resolve().parent.parent / "migrations_ppi"
@pytest.fixture
def ppi_db(tmp_path):
"""Create a temporary PPI database with all migrations applied."""
db_path = tmp_path / "test_ppi.db"
run_ppi_migrations(db_path, MIGRATIONS_DIR)
return db_path
class TestValidateUniprot:
"""Test UniProt accession validation."""
def test_valid_swissprot_p(self):
assert validate_uniprot("P12345") == "P12345"
def test_valid_swissprot_q(self):
assert validate_uniprot("Q9UHC1") == "Q9UHC1"
def test_valid_swissprot_o(self):
assert validate_uniprot("O15553") == "O15553"
def test_valid_trembl_short(self):
assert validate_uniprot("A0A024") == "A0A024"
def test_valid_trembl_long(self):
assert validate_uniprot("A0A0K9P0T2") == "A0A0K9P0T2"
def test_isoform_stripped(self):
assert validate_uniprot("P12345-2") == "P12345"
def test_isoform_long_stripped(self):
assert validate_uniprot("Q9UHC1-14") == "Q9UHC1"
def test_whitespace_stripped(self):
assert validate_uniprot(" P12345 ") == "P12345"
def test_invalid_numeric_only(self):
assert validate_uniprot("12345") is None
def test_invalid_too_short(self):
assert validate_uniprot("P1") is None
def test_invalid_all_alpha(self):
assert validate_uniprot("ABCDEF") is None
def test_invalid_empty(self):
assert validate_uniprot("") is None
def test_invalid_none(self):
assert validate_uniprot(None) is None
def test_invalid_lowercase(self):
assert validate_uniprot("p12345") is None
def test_invalid_special_chars(self):
assert validate_uniprot("P123!5") is None
class TestCanonicalPair:
"""Test canonical pair ordering."""
def test_already_ordered(self):
assert canonical_pair("A00001", "B00002") == ("A00001", "B00002")
def test_reversed(self):
assert canonical_pair("B00002", "A00001") == ("A00001", "B00002")
def test_same_accession(self):
assert canonical_pair("P12345", "P12345") == ("P12345", "P12345")
def test_real_accessions(self):
assert canonical_pair("Q9UHC1", "P12345") == ("P12345", "Q9UHC1")
class TestGetOrInsertProtein:
"""Test protein insertion/retrieval."""
def test_insert_new_protein(self, ppi_db):
conn = get_connection(ppi_db)
try:
pid = get_or_insert_protein(conn, "P12345")
conn.commit()
assert pid == 1
row = conn.execute(
"SELECT uniprot_accession, organism FROM proteins "
"WHERE protein_id = ?",
(pid,),
).fetchone()
assert row[0] == "P12345"
assert row[1] == "Homo sapiens"
finally:
conn.close()
def test_return_existing_protein(self, ppi_db):
conn = get_connection(ppi_db)
try:
pid1 = get_or_insert_protein(conn, "P12345")
conn.commit()
pid2 = get_or_insert_protein(conn, "P12345")
assert pid1 == pid2
count = conn.execute(
"SELECT COUNT(*) FROM proteins"
).fetchone()[0]
assert count == 1
finally:
conn.close()
def test_insert_with_gene_symbol(self, ppi_db):
conn = get_connection(ppi_db)
try:
pid = get_or_insert_protein(conn, "Q9UHC1", gene_symbol="BRCA1")
conn.commit()
row = conn.execute(
"SELECT gene_symbol FROM proteins WHERE protein_id = ?",
(pid,),
).fetchone()
assert row[0] == "BRCA1"
finally:
conn.close()
def test_insert_with_sequence(self, ppi_db):
conn = get_connection(ppi_db)
try:
seq = "MTEYKLVVV"
pid = get_or_insert_protein(conn, "P01116", sequence=seq)
conn.commit()
row = conn.execute(
"SELECT amino_acid_sequence, sequence_length FROM proteins "
"WHERE protein_id = ?",
(pid,),
).fetchone()
assert row[0] == seq
assert row[1] == len(seq)
finally:
conn.close()
def test_insert_without_sequence_null_length(self, ppi_db):
conn = get_connection(ppi_db)
try:
pid = get_or_insert_protein(conn, "P12345")
conn.commit()
row = conn.execute(
"SELECT sequence_length FROM proteins WHERE protein_id = ?",
(pid,),
).fetchone()
assert row[0] is None
finally:
conn.close()
def test_multiple_proteins(self, ppi_db):
conn = get_connection(ppi_db)
try:
pid1 = get_or_insert_protein(conn, "P12345")
pid2 = get_or_insert_protein(conn, "Q9UHC1")
conn.commit()
assert pid1 != pid2
count = conn.execute(
"SELECT COUNT(*) FROM proteins"
).fetchone()[0]
assert count == 2
finally:
conn.close()
|