def test_sortlongest_complex_case3(self):
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
genotypes = [g1]
edgeMap = {1: {10: [20], 30: [10]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot3.calc_depth = 0
expectedAnnot1.calc_depth = 1
expectedAnnot2.calc_depth = 2
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_two_top_parents(self):
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
annot4 = self.createAnnot(40, 'term40')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
g1.mp_headers[0]['annots'].append(annot4)
genotypes = [g1]
# map 10 -> 40, 30-> 20
edgeMap = {1: {10: [40], 30: [20]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot4 = self.createAnnot(40, 'term40')
expectedAnnot1.calc_depth = 0
expectedAnnot2.calc_depth = 1
expectedAnnot3.calc_depth = 0
expectedAnnot4.calc_depth = 1
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot4)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_complex_case3(self):
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
genotypes = [g1]
edgeMap = {1: {10: [20], 30:[10]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot3.calc_depth = 0
expectedAnnot1.calc_depth = 1
expectedAnnot2.calc_depth = 2
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_two_top_parents(self):
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
annot4 = self.createAnnot(40, 'term40')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
g1.mp_headers[0]['annots'].append(annot4)
genotypes = [g1]
# map 10 -> 40, 30-> 20
edgeMap = {1: {10: [40], 30: [20]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot4 = self.createAnnot(40, 'term40')
expectedAnnot1.calc_depth = 0
expectedAnnot2.calc_depth = 1
expectedAnnot3.calc_depth = 0
expectedAnnot4.calc_depth = 1
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot4)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_multiple_headers_different_paths(self):
"""
In one header you have 10->20->30
In the second you only have 40->30
"""
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
# add second header with different paths
g1.mp_headers.append({'term': 'h2', 'annots':[]})
annot3_2 = self.createAnnot(30, 'term30')
annot4 = self.createAnnot(40, 'term40')
g1.mp_headers[1]['annots'].append(annot3_2)
g1.mp_headers[1]['annots'].append(annot4)
genotypes = [g1]
# 10->20->30, 40->30
edgeMap = {1: {10: [20], 20:[30], 40:[30]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot1.calc_depth = 0
expectedAnnot2.calc_depth = 1
expectedAnnot3.calc_depth = 2
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedAnnot3_2 = self.createAnnot(30, 'term30')
expectedAnnot4 = self.createAnnot(40, 'term40')
expectedAnnot4.calc_depth = 0
expectedAnnot3_2.calc_depth = 1
expectedGeno1.mp_headers.append({'term': 'h2', 'annots':[]})
expectedGeno1.mp_headers[1]['annots'].append(expectedAnnot4)
expectedGeno1.mp_headers[1]['annots'].append(expectedAnnot3_2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_multiple_headers_different_paths(self):
"""
In one header you have 10->20->30
In the second you only have 40->30
"""
annot1 = self.createAnnot(10, 'term10')
annot2 = self.createAnnot(20, 'term20')
annot3 = self.createAnnot(30, 'term30')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
g1.mp_headers[0]['annots'].append(annot2)
g1.mp_headers[0]['annots'].append(annot3)
# add second header with different paths
g1.mp_headers.append({'term': 'h2', 'annots': []})
annot3_2 = self.createAnnot(30, 'term30')
annot4 = self.createAnnot(40, 'term40')
g1.mp_headers[1]['annots'].append(annot3_2)
g1.mp_headers[1]['annots'].append(annot4)
genotypes = [g1]
# 10->20->30, 40->30
edgeMap = {1: {10: [20], 20: [30], 40: [30]}}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot2 = self.createAnnot(20, 'term20')
expectedAnnot3 = self.createAnnot(30, 'term30')
expectedAnnot1.calc_depth = 0
expectedAnnot2.calc_depth = 1
expectedAnnot3.calc_depth = 2
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot2)
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot3)
expectedAnnot3_2 = self.createAnnot(30, 'term30')
expectedAnnot4 = self.createAnnot(40, 'term40')
expectedAnnot4.calc_depth = 0
expectedAnnot3_2.calc_depth = 1
expectedGeno1.mp_headers.append({'term': 'h2', 'annots': []})
expectedGeno1.mp_headers[1]['annots'].append(expectedAnnot4)
expectedGeno1.mp_headers[1]['annots'].append(expectedAnnot3_2)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_noedges(self):
annot1 = self.createAnnot(10, 'term10')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
genotypes = [g1]
edgeMap = {}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot1.calc_depth = 0
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
self.assertAnnotSort([expectedGeno1], genotypes)
def test_sortlongest_noedges(self):
annot1 = self.createAnnot(10, 'term10')
g1 = self.createGeno(1)
g1.mp_headers[0]['annots'].append(annot1)
genotypes = [g1]
edgeMap = {}
genotype_mp_hunter._sortAnnotationsByLongestPath(genotypes, edgeMap)
# expected annotations and depths
expectedGeno1 = self.createGeno(1)
expectedAnnot1 = self.createAnnot(10, 'term10')
expectedAnnot1.calc_depth = 0
expectedGeno1.mp_headers[0]['annots'].append(expectedAnnot1)
self.assertAnnotSort([expectedGeno1], genotypes)
