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CLI betas, Methpype full tutorial #7

Merged
merged 24 commits into from
Jul 23, 2019
Merged

CLI betas, Methpype full tutorial #7

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9f3ffd8
exporting beta values for methQC to use
marcmaxson Jul 1, 2019
f7a831a
exporting beta values for methQC to use
marcmaxson Jul 1, 2019
e0bed0a
consolidate_scores function
marcmaxson Jul 2, 2019
6ff251a
consolidate function now part of pipeline --betas
marcmaxson Jul 8, 2019
6721eb6
consolidate part of pipeline
marcmaxson Jul 8, 2019
3beb664
added 27k manifest
Jul 10, 2019
f788af5
added 27K ArrayType
Jul 10, 2019
9b3f4c5
bug fixes: ArrayTYpe to ArrayType and m_factor to m_value
markt Jul 12, 2019
d6dbd66
CLI tweaks
marcmaxson Jul 19, 2019
ef50f60
Merge branch 'feature/beta' of github.com:LifeEGX/methpype into featu…
marcmaxson Jul 19, 2019
90f7b84
Update README.md
Jul 19, 2019
d152f73
Feature/create sample sheet (#4)
Jul 22, 2019
f5ccde5
create_sample_sheet bug fixes
marcmaxson Jul 22, 2019
ea139e5
pipeline processing bugs fixed
marcmaxson Jul 22, 2019
81d50a5
added readthedocs embed and classifiers
Jul 23, 2019
ada07c1
Update setup.py
Jul 23, 2019
b26b5f0
Full tutorial (#6)
Jul 23, 2019
ac207e1
updated links
Jul 23, 2019
55ed189
27k test was wrong
Jul 23, 2019
f8081a2
Update test_array.py
Jul 23, 2019
2c02fdf
Merge branch 'master' into feature/beta
Jul 23, 2019
c51148c
Update test_array.py
Jul 23, 2019
6b2426d
Update test_array.py
Jul 23, 2019
f720308
Update config.yml
Jul 23, 2019
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Update test_array.py
  • Loading branch information
Marc Maxmeister authored Jul 23, 2019
commit c51148cbf43507410d55decd68cbcd8300ddddeb
15 changes: 7 additions & 8 deletions tests/models/test_array.py
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@ def test_inits_correctly(self):
class TestArrayType():
def test_enum_has_correct_values(self):
assert ArrayType.CUSTOM.value == 'custom'
assert ArrayType.ILLUMINA_450K.value == '27k'
assert ArrayType.ILLUMINA_450K.value == '450k'
assert ArrayType.ILLUMINA_EPIC.value == 'epic'
assert ArrayType.ILLUMINA_EPIC_PLUS.value == 'epic+'
Expand All @@ -32,15 +33,13 @@ def test_out_of_range_probe_counts_throws(self, capsys):
captured = capsys.readouterr()
assert captured.out == 'Unknown array type\n'

def test_27k_probe_counts_lower_bound_throws(self):
with pytest.raises(ValueError):
array_type = ArrayType.from_probe_count(54000)
assert array_type == ArrayType.ILLUMINA_27K
def test_27k_probe_counts_lower_bound(self):
array_type = ArrayType.from_probe_count(54000)
assert array_type == ArrayType.ILLUMINA_27K

def test_27k_probe_counts_upper_bound_throws(self):
with pytest.raises(ValueError):
array_type = ArrayType.from_probe_count(56000)
assert array_type == ArrayType.ILLUMINA_27K
def test_27k_probe_counts_upper_bound(self):
array_type = ArrayType.from_probe_count(56000)
assert array_type == ArrayType.ILLUMINA_27K

def test_450k_probe_counts_lower_bound(self):
array_type = ArrayType.from_probe_count(622000)
Expand Down