def test_find_closest_gene(self):
r = ReorderGenes([], [], {})
gf = {
'abc': GeneToFiles('abc', gene_to_files=[0, 2, 2, 0]),
'efg': GeneToFiles('efg', gene_to_files=[2, 2, -2, 0]),
'geneA': GeneToFiles('geneA', gene_to_files=[0, 2, 2, 0]),
'outlier': GeneToFiles('outlier', gene_to_files=[0, 0, 0, 1])
}
self.assertEqual('abc', r.find_closest_gene('geneA', gf))
self.assertEqual('abc', r.find_closest_gene('efg', gf))
self.assertEqual('efg', r.find_closest_gene('abc', gf))
self.assertEqual('abc', r.find_closest_gene('outlier', gf))
def create_gene_file_objects(self):
genes_to_files = {}
for i, g in enumerate(self.gene_names):
logfc = []
for report_file in self.genereports:
logfc.append(int(self.reports_to_gene_logfc[report_file][i]))
gf = GeneToFiles(g, gene_to_files=logfc)
if gf.number_of_files > 0:
genes_to_files[g] = gf
return genes_to_files
def test_all(self):
g = GeneToFiles('abc', gene_to_files=[2, 11, 10, -15])
self.assertEqual(4, g.number_of_files)
def test_one(self):
g = GeneToFiles('abc', gene_to_files=[0, 11, 0, 0])
self.assertEqual(1, g.number_of_files)
def test_empty(self):
g = GeneToFiles('abc', gene_to_files=[0, 0, 0, 0])
self.assertEqual(0, g.number_of_files)
def test_common_counting(self):
g1 = GeneToFiles('abc', gene_to_files=[0, 11, 13, 0])
g2 = GeneToFiles('efg', gene_to_files=[0, 11, -12, 0])
r = ReorderGenes([], [], {})
self.assertEqual(2, r.files_in_common(g1, g2))