import sqlite3
from phizz.database import (populate_hpo, populate_disease, get_cursor)
from phizz.log import configure_stream
configure_stream(level="DEBUG")
schema_filename = "tests/fixtures/schema.sql"
def test_populate_hpo(connection, hpo_terms, mim_terms):
"""docstring for test_populate_hpo"""
populate_hpo(
connection=connection,
hpo_terms=hpo_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from hpo where hpo_id = '1459'")
for row in cursor.fetchmany():
assert row['description'] == "1-3 toe syndactyly"
assert row['name'] == "HP:0001459"
def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
"""Functions to prepare infiles from different sources to phizz format"""
import os
import sys
import logging
import gzip
import logging
from codecs import open
import click
from phizz.log import configure_stream
from phizz.utils import parse_genes
configure_stream('INFO')
logger = logging.getLogger(__name__)
def uniqify_phenotypes(lines):
"""Produce a new resource with phenotypes and descriptions
Args:
lines (Iterator): The lines of the file
Returns:
hpo_terms(generator(dict)): The hpoterms
"""
hpo_terms = {}
for line in lines:
if not line.startswith('#'):
line = line.rstrip().split('\t')
import sqlite3
from phizz.database import (populate_hpo, populate_disease, get_cursor)
from phizz.log import configure_stream
configure_stream(level="DEBUG")
schema_filename = "tests/fixtures/schema.sql"
def test_populate_hpo(connection, hpo_terms, mim_terms):
"""docstring for test_populate_hpo"""
populate_hpo(
connection=connection,
hpo_terms=hpo_terms,
)
cursor = get_cursor(connection=connection)
cursor.execute("SELECT * from hpo where hpo_id = '1459'")
for row in cursor.fetchmany():
assert row['description'] == "1-3 toe syndactyly"
assert row['name'] == "HP:0001459"
def test_get_hpo_from_omim(connection, hpo_terms, mim_terms):
"""docstring for test_get_description"""
populate_disease(
connection=connection,
disease_terms=mim_terms,
)
import sqlite3
import pytest
from phizz.database import (populate_hpo, populate_disease, populate_genes,
get_database)
from phizz.utils import (parse_phenotypes, parse_diseases, parse_genes)
from phizz.log import configure_stream
logger = configure_stream(level="DEBUG")
SCHEMA = 'tests/fixtures/schema.sql'
@pytest.fixture(scope="function")
def mim_terms(request):
"""Get mim terms"""
mim_lines = [
"#Format: diseaseId<tab>gene-symbol<tab>gene-id(entrez)<tab>HPO-ID<tab>HPO-term-name",
"OMIM:600920\tSCARF2\t91179\tHP:0000767\tPectus excavatum",
"OMIM:600920\tSCARF2\t91179\tHP:0003042\tElbow dislocation",
"OMIM:600920\tSCARF2\t91179\tHP:0005280\tDepressed nasal bridge",
"OMIM:600920\tSCARF2\t91179\tHP:0001363\tCraniosynostosis",
"OMIM:600920\tSCARF2\t91179\tHP:0000772\tAbnormality of the ribs",
"OMIM:600920\tSCARF2\t91179\tHP:0001195\tSingle umbilical artery",
"OMIM:600920\tSCARF2\t91179\tHP:0002987\tElbow flexion contracture",
"OMIM:613376\tHSPB3\t8988\tHP:0000006\tAutosomal dominant inheritance",
"OMIM:613376\tHSPB3\t8988\tHP:0002355\tDifficulty walking",
"OMIM:613376\tHSPB3\t8988\tHP:0002600\tHyporeflexia of lower limbs",
"OMIM:613376\tHSPB3\t8988\tHP:0003445\tEMG: neuropathic changes",
"OMIM:613376\tHSPB3\t8988\tHP:0009830\tPeripheral neuropathy",
"OMIM:613376\tHSPB3\t8988\tHP:0003376\tSteppage gait",
