def test_compute_pathways_coverage_structured(self):
"""
Test the compute_pathways_coverage function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with structured pathways
"""
# Set xipe to off
config.xipe_toggle = "off"
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway_structure("pathway1", " A B C D ")
pathways_database_store.add_pathway_structure("pathway2",
" A B C D E F ")
# Have all test data be from the same bug
bug = "bug"
pathways_and_reactions_store = store.PathwaysAndReactions()
# Just a note that a value of 1 has a chi2cdf value of 0
# Also values ~10 or less have small chi2cdf values
pathways_and_reactions_store.add(bug, "A", "pathway1", 11)
pathways_and_reactions_store.add(bug, "B", "pathway1", 12)
pathways_and_reactions_store.add(bug, "C", "pathway1", 13)
pathways_and_reactions_store.add(bug, "D", "pathway1", 14)
pathways_and_reactions_store.add(bug, "A", "pathway2", 19)
pathways_and_reactions_store.add(bug, "B", "pathway2", 20)
pathways_and_reactions_store.add(bug, "C", "pathway2", 30)
pathways_and_reactions_store.add(bug, "D", "pathway2", 40)
pathways_and_reactions_store.add(bug, "E", "pathway2", 50)
pathways_and_reactions_store.add(bug, "F", "pathway2", 60)
# Get the coverage result
# The median is the median of all of the reactions of all of the pathways for this bug
median_score_value = 19.5
# boost the pathway values
pathway1_values_boosted = [12, 12, 13, 14]
coverage_pathway1 = len(pathway1_values_boosted) / sum(
1.0 / chi2cdf.chi2cdf(v, median_score_value)
for v in pathway1_values_boosted)
pathway2_values_boosted = [20, 20, 30, 40, 50, 60]
coverage_pathway2 = len(pathway2_values_boosted) / sum(
1.0 / chi2cdf.chi2cdf(v, median_score_value)
for v in pathway2_values_boosted)
# Find the actual result
pathways_abundance_store_result = modules.compute_pathways_coverage(
pathways_and_reactions_store, pathways_database_store)
# Test the pathways abundance match those expected
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway1"),
coverage_pathway1)
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway2"),
coverage_pathway2)
def test_compute_pathways_coverage_unstructured(self):
"""
Test the compute_pathways_coaverage function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with unstructured pathways
"""
# Set xipe to off
config.xipe_toggle = "off"
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway("pathway1", ["A", "B", "C", "D"])
pathways_database_store.add_pathway("pathway2",
["A", "B", "C", "D", "E", "F"])
# Have all test data be from the same bug
bug = "bug"
pathways_and_reactions_store = store.PathwaysAndReactions()
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
# Note B is not recored for pathway1 which will result in a zero value
pathways_and_reactions_store.add(bug, "C", "pathway1", 3)
pathways_and_reactions_store.add(bug, "D", "pathway1", 40)
pathways_and_reactions_store.add(bug, "A", "pathway2", 10)
pathways_and_reactions_store.add(bug, "B", "pathway2", 20)
# Note C is not recored for pathway2 which will result in a zero value
pathways_and_reactions_store.add(bug, "D", "pathway2", 40)
pathways_and_reactions_store.add(bug, "E", "pathway2", 50)
# Note F is not recored for pathway2 which will result in a zero value
# The coverage for each pathway if the number of reactions greater than the median
# divided by the total reactions in the pathway
# The median for this set is 20
pathway1_values = [0, 1, 3, 40]
count_greater_than_median = 1
pathway1_coverage = count_greater_than_median / float(
len(pathway1_values))
pathway2_values = [0, 0, 10, 20, 40, 50]
count_greater_than_median = 2
pathway2_coverage = count_greater_than_median / float(
len(pathway2_values))
pathways_coverage_store_result = modules.compute_pathways_coverage(
pathways_and_reactions_store, pathways_database_store)
# Test the pathways abundance match those expected
self.assertEqual(
pathways_coverage_store_result.get_score_for_bug(bug, "pathway1"),
pathway1_coverage)
self.assertEqual(
pathways_coverage_store_result.get_score_for_bug(bug, "pathway2"),
pathway2_coverage)
def test_compute_pathways_abundance_unstructured(self):
"""
Test the compute_pathways_abundance function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with unstructured pathways
"""
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway("pathway1", ["A", "B", "C", "D"])
pathways_database_store.add_pathway("pathway2",
["A", "B", "C", "D", "E", "F"])
# Have all test data be from the same bug
bug = "bug"
pathways_and_reactions_store = store.PathwaysAndReactions()
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
# Note B is not recored for pathway1 which will result in a zero value
pathways_and_reactions_store.add(bug, "C", "pathway1", 3)
pathways_and_reactions_store.add(bug, "D", "pathway1", 4)
pathways_and_reactions_store.add(bug, "A", "pathway2", 10)
pathways_and_reactions_store.add(bug, "B", "pathway2", 20)
# Note C is not recored for pathway2 which will result in a zero value
pathways_and_reactions_store.add(bug, "D", "pathway2", 40)
pathways_and_reactions_store.add(bug, "E", "pathway2", 50)
# Note F is not recored for pathway2 which will result in a zero value
# The abundance for each pathway is the average of the largest half of the reaction values
# For unstructured pathways, if the reaction is not included it does not result in a zero abundance
pathway1_values = [0, 1, 3, 4]
pathway1_abundance_set = pathway1_values[int(len(pathway1_values) /
2):]
pathway1_abundance = sum(pathway1_abundance_set) / len(
pathway1_abundance_set)
pathway2_values = [0, 0, 10, 20, 40, 50]
pathway2_abundance_set = pathway2_values[int(len(pathway2_values) /
2):]
pathway2_abundance = sum(pathway2_abundance_set) / len(
pathway2_abundance_set)
pathways_abundance_store_result, reactions_in_pathways_present = modules.compute_pathways_abundance(
pathways_and_reactions_store, pathways_database_store)
# Test the pathways abundance match those expected
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway1"),
pathway1_abundance)
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway2"),
pathway2_abundance)
def test_compute_pathways_abundance_structured(self):
"""
Test the compute_pathways_abundance function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with structured pathways
"""
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway_structure("pathway1", " A B C D ")
pathways_database_store.add_pathway_structure("pathway2",
" A B C D E F ")
# Have all test data be from the same bug
bug = "bug"
pathways_and_reactions_store = store.PathwaysAndReactions()
# Just a note that a value of 1 has a chi2cdf value of 0
# Also values ~10 or less have small chi2cdf values
pathways_and_reactions_store.add(bug, "A", "pathway1", 11)
pathways_and_reactions_store.add(bug, "B", "pathway1", 12)
pathways_and_reactions_store.add(bug, "C", "pathway1", 13)
pathways_and_reactions_store.add(bug, "D", "pathway1", 14)
pathways_and_reactions_store.add(bug, "A", "pathway2", 19)
pathways_and_reactions_store.add(bug, "B", "pathway2", 20)
pathways_and_reactions_store.add(bug, "C", "pathway2", 30)
pathways_and_reactions_store.add(bug, "D", "pathway2", 40)
pathways_and_reactions_store.add(bug, "E", "pathway2", 50)
pathways_and_reactions_store.add(bug, "F", "pathway2", 60)
# The abundance for each pathway is the harmonic mean of the values
# boost the lowest value in the pathway
pathway1_values_boosted = [12, 12, 13, 14]
pathway1_abundance = len(pathway1_values_boosted) / sum(
1.0 / v for v in pathway1_values_boosted)
pathway2_values_boosted = [20, 20, 30, 40, 50, 60]
pathway2_abundance = len(pathway2_values_boosted) / sum(
1.0 / v for v in pathway2_values_boosted)
# Find the actual result
pathways_abundance_store_result, reactions_in_pathways_present = modules.compute_pathways_abundance(
pathways_and_reactions_store, pathways_database_store)
# Test the pathways abundance match those expected
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway1"),
pathway1_abundance)
self.assertEqual(
pathways_abundance_store_result.get_score_for_bug(bug, "pathway2"),
pathway2_abundance)
def test_PathwaysAndReactions_max_median_score_even_number_vary_reactions(self):
"""
Pathways and Reactions class: Test add and max median score
Test an even number of values and different reactions
"""
pathways_and_reactions=store.PathwaysAndReactions()
# add scores all for same pathway and different reaction
pathways_and_reactions.add("bug","R1","P1",1)
pathways_and_reactions.add("bug","R2","P1",2)
pathways_and_reactions.add("bug","R3","P1",3)
pathways_and_reactions.add("bug","R4","P1",4)
# test median score for an even number of values
self.assertEqual(pathways_and_reactions.max_median_score("bug"),4)
def test_compute_pathways_abundance_unstructured_reactions_list(self):
"""
Test the compute_pathways_abundance function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with unstructured pathways
Test the resulting list of reactions included in pathways
"""
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway("pathway1", ["A", "B", "C", "D"])
pathways_database_store.add_pathway("pathway2",
["A", "B", "C", "D", "E", "F"])
pathways_database_store.add_pathway("pathway3", ["A", "B", "G"])
# Have all test data be from two bugs
bug = "bug1"
pathways_and_reactions_store = store.PathwaysAndReactions()
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
pathways_and_reactions_store.add(bug, "B", "pathway1", 2)
pathways_and_reactions_store.add(bug, "B", "pathway2", 2)
pathways_and_reactions_store.add(bug, "C", "pathway2", 3)
expected_reactions_in_pathways_present = {}
expected_reactions_in_pathways_present[bug] = ["A", "B", "C"]
bug = "bug2"
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
pathways_and_reactions_store.add(bug, "D", "pathway1", 3)
pathways_and_reactions_store.add(bug, "B", "pathway1", 2)
pathways_and_reactions_store.add(bug, "B", "pathway2", 2)
expected_reactions_in_pathways_present[bug] = ["A", "B", "D"]
pathways_abundance_store_result, reactions_in_pathways_present = modules.compute_pathways_abundance(
pathways_and_reactions_store, pathways_database_store)
# Test the reactions match those expected
self.assertEqual(
sorted(expected_reactions_in_pathways_present["bug1"]),
sorted(list(reactions_in_pathways_present["bug1"])))
self.assertEqual(
sorted(expected_reactions_in_pathways_present["bug2"]),
sorted(list(reactions_in_pathways_present["bug2"])))
def test_PathwaysAndReactions_median_score_odd_number_vary_pathways(self):
"""
Pathways and Reactions class: Test add and median score
Test an odd number of values and different pathways
"""
pathways_and_reactions=store.PathwaysAndReactions()
# add scores all for same pathway and reaction
pathways_and_reactions.add("bug","R1","P1",1)
pathways_and_reactions.add("bug","R1","P2",2)
pathways_and_reactions.add("bug","R1","P3",3)
pathways_and_reactions.add("bug","R1","P4",4)
pathways_and_reactions.add("bug","R1","P5",5)
# test median score for odd number of values
self.assertEqual(pathways_and_reactions.median_score("bug"),3)
def test_compute_pathways_abundance_structured_reactions_list(self):
"""
Test the compute_pathways_abundance function
Test PathwaysDatabase add
Test PathwaysAndReactions store
Test Pathways store
Test with structured pathways
Test gap fill
Test the resulting list of reactions included in pathways
"""
# Create the database structure
pathways_database_store = store.PathwaysDatabase()
pathways_database_store.add_pathway_structure("pathway1", " A B C D ")
pathways_database_store.add_pathway_structure("pathway2",
" A B C D E F ")
pathways_database_store.add_pathway_structure("pathway3", " A B G")
# Have all test data be from three bugs
bug = "bug1"
pathways_and_reactions_store = store.PathwaysAndReactions()
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
pathways_and_reactions_store.add(bug, "B", "pathway1", 2)
pathways_and_reactions_store.add(bug, "C", "pathway1", 3)
expected_reactions_in_pathways_present = {}
# This pathway is present because D is filled in
# Though D does not have abundance so it is not included in the list
expected_reactions_in_pathways_present[bug] = ["A", "B", "C"]
bug = "bug2"
pathways_and_reactions_store.add(bug, "A", "pathway1", 1)
pathways_and_reactions_store.add(bug, "B", "pathway1", 3)
pathways_and_reactions_store.add(bug, "D", "pathway2", 2)
pathways_and_reactions_store.add(bug, "B", "pathway2", 2)
# The pathways for this bug are missing too many reactions to have abundance
expected_reactions_in_pathways_present[bug] = []
bug = "bug3"
pathways_and_reactions_store.add(bug, "A", "pathway3", 1)
pathways_and_reactions_store.add(bug, "B", "pathway3", 3)
pathways_and_reactions_store.add(bug, "G", "pathway3", 2)
pathways_and_reactions_store.add(bug, "B", "pathway2", 2)
# One pathway for this bug includes all reactions
expected_reactions_in_pathways_present[bug] = ["A", "B", "G"]
pathways_abundance_store_result, reactions_in_pathways_present = modules.compute_pathways_abundance(
pathways_and_reactions_store, pathways_database_store)
# Test the reactions match those expected
self.assertEqual(
sorted(expected_reactions_in_pathways_present["bug1"]),
sorted(list(reactions_in_pathways_present["bug1"])))
self.assertEqual(
sorted(expected_reactions_in_pathways_present["bug2"]),
sorted(list(reactions_in_pathways_present["bug2"])))
self.assertEqual(
sorted(expected_reactions_in_pathways_present["bug3"]),
sorted(list(reactions_in_pathways_present["bug3"])))