def test_reorder_genes(self):
r = ReorderGenes(
['geneA', 'geneB', 'geneC'], ['file1', 'file2', 'file3', 'file4'],
{
'file1': [0, 0, 9],
'file2': [9, -9, 9],
'file3': [0, 5, 9],
'file4': [1, 0, 1]
})
self.assertEqual(['geneC', 'geneA', 'geneB'], r.reorder_genes())
def test_zeros(self):
r = ReorderGenes(
['geneA', 'geneB', 'geneC'], ['file1', 'file2', 'file3', 'file4'],
{
'file1': [0, 0, 0],
'file2': [0, 0, 0],
'file3': [0, 0, 0],
'file4': [0, 0, 0]
})
self.assertEqual(None, r.get_highest_freq(r.genes_to_files))
def test_valid(self):
r = ReorderGenes(
['geneA', 'geneB', 'geneC'], ['file1', 'file2', 'file3', 'file4'],
{
'file1': [0, 0, 9],
'file2': [9, -9, 9],
'file3': [0, 5, 9],
'file4': [1, 0, 1]
})
self.assertEqual('geneC', r.get_highest_freq(r.genes_to_files))
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 run(self):
self.features = EMBLReader(self.emblfile).features
self.gene_names = self.generate_gene_names()
self.reports_to_gene_logfc = self.create_reports_to_gene_logfc(
self.gene_names)
self.filtered_gene_names = ReorderGenes(
self.gene_names, self.genereports,
self.reports_to_gene_logfc).reorder_genes()
self.filtered_reports_to_gene_logfc = self.create_reports_to_gene_logfc(
self.filtered_gene_names)
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))