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test agp creation with valid data and no mocks
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@IvoStefanov
IvoStefanov committed Nov 10, 2023
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338 changes: 311 additions & 27 deletions dae/dae/autism_gene_profile/tests/test_generate_autism_gene_profile.py
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# pylint: disable=W0621,C0114,C0116,W0212,W0613
import pathlib

import textwrap
import pytest
import yaml
from pytest_mock import MockerFixture

from dae.testing.import_helpers import vcf_study
from dae.genomic_resources.testing import \
setup_directories, setup_pedigree, setup_vcf
from dae.testing.t4c8_import import t4c8_gpf
from dae.autism_gene_profile.generate_autism_gene_profile import main
from dae.autism_gene_profile.db import AutismGeneProfileDB
from dae.gpf_instance import GPFInstance


@pytest.mark.xfail(reason="requires environment setup")
@pytest.fixture
def local_agp_config() -> str:
return yaml.dump({
"order": [
"gene_set_rank",
"gene_score",
"study_1",
],
"default_dataset": "study_1",
"gene_sets": [
{
"category": "gene_set",
"display_name": "test gene sets",
"sets": [
{
"set_id": "test_gene_set_1",
"collection_id": "gene_sets"
},
{
"set_id": "test_gene_set_2",
"collection_id": "gene_sets"
},
{
"set_id": "test_gene_set_3",
"collection_id": "gene_sets"
},
]
},
],
"genomic_scores": [
{
"category": "gene_score",
"display_name": "Test gene score",
"scores": [
{"score_name": "gene_score1", "format": "%%s"},
]
}
],
"datasets": {
"study_1": {
"statistics": [
{
"id": "lgds",
"display_name": "LGDs",
"effects": ["lgds"],
"category": "denovo"
},
{
"id": "denovo_missense",
"display_name": "Missense",
"effects": ["missense"],
"category": "denovo"
}
],
"person_sets": [
{
"set_name": "autism",
"collection_name": "phenotype"
},
{
"set_name": "unaffected",
"collection_name": "phenotype"
},
]
}
}
}, default_flow_style=False)


@pytest.fixture
def local_gpf_instance(
local_agp_config: str,
tmp_path: pathlib.Path) -> None:
setup_directories(
tmp_path,
{
"gpf_instance": {
"agp_config.yaml": local_agp_config,
"gpf_instance.yaml": textwrap.dedent("""
autism_gene_tool_config:
conf_file: "agp_config.yaml"
gene_sets_db:
gene_set_collections:
- gene_sets
gene_scores_db:
gene_scores:
- gene_score1
"""),
},
"gene_sets": {
"genomic_resource.yaml": textwrap.dedent("""
type: gene_set
id: gene_sets
format: directory
directory: test_gene_sets
web_label: test gene sets
web_format_str: "key| (|count|): |desc"
"""),
"test_gene_sets": {
"test_gene_set_1.txt": textwrap.dedent("""
test_gene_set_1
contains t4
t4
"""),
"test_gene_set_2.txt": textwrap.dedent("""
test_gene_set_2
contains c8
c8
"""),
"test_gene_set_3.txt": textwrap.dedent("""
test_gene_set_3
contains t4 and c8
t4
c8
"""),
}
},
"gene_score1": {
"genomic_resource.yaml": textwrap.dedent("""
type: gene_score
filename: score.csv
scores:
- id: gene_score1
desc: Test gene score
histogram:
type: number
number_of_bins: 100
view_range:
min: 0.0
max: 30.0
"""),
"score.csv": textwrap.dedent("""
gene,gene_score1
t4,10
c8,20
"""),
},
}
)

ped_path = setup_pedigree(
tmp_path / "study_1" / "pedigree" / "in.ped",
"""
familyId personId dadId momId sex status role
f1.1 mom1 0 0 2 1 mom
f1.1 dad1 0 0 1 1 dad
f1.1 ch1 dad1 mom1 2 2 prb
f1.3 mom3 0 0 2 1 mom
f1.3 dad3 0 0 1 1 dad
f1.3 ch3 dad3 mom3 2 1 prb
""")
vcf_path = setup_vcf(
tmp_path / "study_1" / "vcf" / "in.vcf.gz",
"""
##fileformat=VCFv4.2
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##contig=<ID=chr1>
##contig=<ID=chr2>
##contig=<ID=chr3>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT mom1 dad1 ch1 mom3 dad3 ch3
chr1 15 . AG A . . . GT 0/0 0/0 0/1 0/0 0/0 0/0
chr1 15 . A C . . . GT 0/0 0/0 0/0 0/0 0/0 0/1
chr1 35 . G A . . . GT 0/0 0/0 0/1 0/0 0/0 0/0
chr1 35 . G C . . . GT 0/0 0/0 0/0 0/0 0/0 0/1
chr1 126 . T A . . . GT 0/0 0/0 0/1 0/0 0/0 0/0
chr1 135 . T A . . . GT 0/0 0/0 0/0 0/0 0/0 0/1
chr1 165 . G T . . . GT 0/0 0/1 0/1 0/0 0/0 0/0
chr1 195 . C T . . . GT 0/0 0/0 0/1 0/0 0/0 0/0
""") # noqa

project_config_update = {
"input": {
"vcf": {
"denovo_mode": "denovo",
"omission_mode": "omission",
}
},
}

instance = t4c8_gpf(tmp_path)

vcf_study(
tmp_path,
"study_1", ped_path, [vcf_path],
instance,
project_config_update=project_config_update,
study_config_update={
"conf_dir": str(tmp_path / "study_1"),
"person_set_collections": {
"phenotype": {
"id": "phenotype",
"name": "Phenotype",
"sources": [
{
"from": "pedigree",
"source": "status"
}
],
"default": {
"color": "#aaaaaa",
"id": "unspecified",
"name": "unspecified",
},
"domain": [
{
"color": "#bbbbbb",
"id": "autism",
"name": "autism",
"values": [
"affected"
]
},
{
"color": "#00ff00",
"id": "unaffected",
"name": "unaffected",
"values": [
"unaffected"
]
},
]
},
"selected_person_set_collections": [
"phenotype"
]
}
})

return instance


def test_generate_autism_gene_profile(
local_gpf_instance: GPFInstance,
tmp_path: pathlib.Path, mocker: MockerFixture) -> None:
tmp_path: pathlib.Path) -> None:
agpdb_filename = str(tmp_path / "agpdb")
argv = [
"--dbfile",
agpdb_filename,
"-vv",
"--genes",
"PCDHA4",
]

# local_gpf_instance._autism_gene_profile_config = local_agp_config
main(local_gpf_instance, argv)
agpdb = AutismGeneProfileDB(
local_gpf_instance._autism_gene_profile_config,
agpdb_filename,
clear=False
)
agp = agpdb.get_agp("PCDHA4")
assert agp is not None
t4 = agpdb.get_agp("t4")
c8 = agpdb.get_agp("c8")

counts = agp.variant_counts["iossifov_2014"]
assert counts is not None
assert t4.gene_sets == [
"gene_sets_test_gene_set_1",
"gene_sets_test_gene_set_3"
]
assert c8.gene_sets == [
"gene_sets_test_gene_set_2",
"gene_sets_test_gene_set_3"
]

unknown = counts["autism"]
assert unknown["denovo_noncoding"] == {
"count": 1,
"rate": 90.9090909090909
}
assert unknown["denovo_missense"] == {
"count": 0,
"rate": 0.0
assert t4.genomic_scores == {
"gene_score": {
"gene_score1": {
"format": "%s",
"value": 10.0
}
}
}

counts = agp.variant_counts["iossifov_2014"]
assert counts is not None
assert c8.genomic_scores == {
"gene_score": {
"gene_score1": {
"format": "%s",
"value": 20.0
}
}
}

unaffected = counts["unaffected"]
assert unaffected["denovo_noncoding"] == {
"count": 0,
"rate": 0.0
assert t4.variant_counts == {
"study_1": {
"autism": {
"lgds": {
"count": 1.0,
"rate": 1000.0
},
"denovo_missense": {
"count": 1.0,
"rate": 1000.0
}
},
"unaffected": {
"lgds": {
"count": 0.0,
"rate": 0.0
},
"denovo_missense": {
"count": 2.0,
"rate": 2000.0
}
}
}
}
assert unaffected["denovo_missense"] == {
"count": 0,
"rate": 0.0

assert c8.variant_counts == {
"study_1": {
"autism": {
"lgds": {
"count": 1.0,
"rate": 1000.0
},
"denovo_missense": {
"count": 1.0,
"rate": 1000.0
}
},
"unaffected": {
"lgds": {
"count": 1.0,
"rate": 1000.0
},
"denovo_missense": {
"count": 0.0,
"rate": 0.0
}
}
}
}

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