test_commands.py

import pytest
from tempfile import NamedTemporaryFile, TemporaryDirectory, mkdtemp
from gseapy.gsea import gsea, prerank, ssgsea, replot
from gseapy.enrichr import enrichr

@pytest.fixture
def edbDIR():
    return "tests/data"

@pytest.fixture
def genelist():
    return "tests/data/gene_list.txt"

@pytest.fixture
def gseaGCT():
    return "tests/data/P53_resampling_data.txt"

@pytest.fixture
def gseaCLS():
    return "tests/data/P53.cls"

@pytest.fixture
def prernk():
    return "tests/data/edb/gsea_data.gsea_data.rnk"

@pytest.fixture
def geneGMT():
    return "tests/data/genes.gmt"

@pytest.fixture
def ssGMT():
    return "tests/data/randomSets.gmt"

@pytest.fixture
def ssGCT():
    return "tests/data/testSet_rand1200.gct"

def test_gsea(gseaGCT, gseaCLS, geneGMT):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    gsea(data=gseaGCT, gene_sets=geneGMT, cls=gseaCLS,
         outdir=tmpdir.name, permutation_type='phenotype',
         permutation_num=10)
    tmpdir.cleanup()


def test_prerank(prernk, geneGMT):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    prerank(prernk, geneGMT, tmpdir.name, permutation_num=10)
    tmpdir.cleanup()
    prerank(prernk, geneGMT, None, permutation_num=10)


def test_ssgsea1(ssGCT, geneGMT):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    ssgsea(ssGCT, geneGMT, tmpdir.name, permutation_num=100)
    tmpdir.cleanup()

def test_ssgsea2(ssGCT, geneGMT):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    ssgsea(ssGCT, geneGMT, tmpdir.name, permutation_num=0)
    tmpdir.cleanup()
    ssgsea(ssGCT, geneGMT, None, permutation_num=0)

def test_enrichr(genelist, geneGMT):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    enrichr(genelist, gene_sets=['KEGG_2016', geneGMT], outdir=tmpdir.name)
    tmpdir.cleanup()
    enrichr(genelist, gene_sets='KEGG_2013,KEGG_2016', outdir=None)

def test_replot(edbDIR):
    # Only tests of the command runs successfully,
    # doesnt't check the image
    tmpdir= TemporaryDirectory(dir="tests")
    replot(edbDIR, tmpdir.name)
    tmpdir.cleanup()