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 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",