diff --git a/src/nleval/data/network/funcoup.py b/src/nleval/data/network/funcoup.py index 7ae49495..663c7a2c 100644 --- a/src/nleval/data/network/funcoup.py +++ b/src/nleval/data/network/funcoup.py @@ -7,8 +7,6 @@ class FunCoup(BaseNDExData): The edge weights are PFC values, which is a probabilistic estimation about whether a pair of genes are functionally coupled. - - https://funcoup5.scilifelab.se/help/#Citation """ diff --git a/src/nleval/label/filters/nonred.py b/src/nleval/label/filters/nonred.py index 8e0599b6..cbef979b 100644 --- a/src/nleval/label/filters/nonred.py +++ b/src/nleval/label/filters/nonred.py @@ -11,7 +11,8 @@ class LabelsetNonRedFilter(BaseFilter): """Filter out redundant labelsets in a labelset collection. The detailed procedure can be found in the supplementary data of - https://doi.org/10.1093/bioinformatics/btaa150 In brief, given a labelset + https://doi.org/10.1093/bioinformatics/btaa150 + In brief, given a labelset collection, a graph of labelsets if first constructed based on the redundancy score function of interest. Here, we use the combination of Jaccard index and overlap coefficient. Then, for each connected component in diff --git a/test/test_graph.py b/test/test_graph.py index 8517adcb..7561d4ce 100755 --- a/test/test_graph.py +++ b/test/test_graph.py @@ -1120,15 +1120,7 @@ def test_restrict_to_branch(self): self.assertRaises(IDNotExistError, graph.restrict_to_branch, "g") def test_read_obo(self): - r""" - - a - / | \ - b c (x, y) d - | \ / - e [z] f - - """ + r"""A / | \ b c (x, y) d | \ / e [z] f.""" obo_path = osp.join(SAMPLE_DATA_DIR, "toy_ontology.obo") with self.subTest(xref_prefix=None): # Do not capture xref when xref_prefix is unset diff --git a/test/test_label/filters/test_nonred.py b/test/test_label/filters/test_nonred.py index b605a5de..65452440 100644 --- a/test/test_label/filters/test_nonred.py +++ b/test/test_label/filters/test_nonred.py @@ -14,14 +14,10 @@ def case1(): r"""Labelset collection test case 1. - When threshold is set to 0.49, and use overlap (or threshold set to 0.3 - and use jaccard): - - lb0 - | \ - lb1 lb2 - | - lb3 + When threshold is set to 0.49, and use overlap (or threshold set to 0.3 and + use jaccard): + + lb0 | \ lb1 lb2 | lb3 The expected outcome is thus: ['lb0', 'lb3']