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"""module contains python code for wgcna"""
from unittest import skip
from unittest import TestCase
from unittest import mock
from gn3.computations.wgcna import dump_wgcna_data
from gn3.computations.wgcna import compose_wgcna_cmd
from gn3.computations.wgcna import call_wgcna_script
class TestWgcna(TestCase):
"""test class for wgcna"""
@mock.patch("gn3.computations.wgcna.dump_wgcna_data")
def test_call_wgcna_script(self, mock_dump):
"""call wgcna script"""
mock_dump.return_value = "/tmp/QmQPeNsJPyVWPFDVHb77w8G42Fvo15z4bG2X8D2GhfbSXc-test.json"
results = call_wgcna_script(
"/home/kabui/project/genenetwork3/scripts/wgcna_analysis.R", {})
self.assertEqual(results, "dsedf")
def test_compose_wgcna_cmd(self):
"""test for composing wgcna cmd"""
wgcna_cmd = compose_wgcna_cmd(
"wgcna.r", "/tmp/wgcna.json")
self.assertEqual(
wgcna_cmd, "Rscript ./scripts/wgcna.r /tmp/wgcna.json")
@skip("to update tests")
def test_create_json_file(self):
"""test for writing the data to a csv file"""
# # All the traits we have data for (should not contain duplicates)
# All the strains we have data for (contains duplicates)
trait_sample_data = {"1425642_at": {"129S1/SvImJ": 7.142,
"A/J": 7.31, "AKR/J": 7.49,
"B6D2F1": 6.899, "BALB/cByJ": 7.172,
"BALB/cJ": 7.396},
"1457784_at": {"129S1/SvImJ": 7.071, "A/J": 7.05,
"AKR/J": 7.313,
"B6D2F1": 6.999, "BALB/cByJ": 7.293,
"BALB/cJ": 7.117},
"1444351_at": {"129S1/SvImJ": 7.221, "A/J": 7.246,
"AKR/J": 7.754,
"B6D2F1": 6.866, "BALB/cByJ": 6.752,
"BALB/cJ": 7.269}
}
expected_input = {
"trait_sample_data": trait_sample_data,
"TOMtype": "unsigned",
"minModuleSize": 30
}
results = dump_wgcna_data(
expected_input)
self.assertEqual(results, {})
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