def test_gene_families_tsv_output_with_names(self):
"""
Test the gene families function and the blast config indexes
Test UniRef50_unknown is read in and used for gene scores but not printed
Test the tsv output
Test that gene families have names applied to them
Test unmapped reads total is written with the same precision as other lines
"""
# update the max decimals to allow for rounding
config.output_max_decimals = 7
# set to a smaller mapping file
original_gene_family_mapping_file = config.gene_family_name_mapping_file
config.gene_family_name_mapping_file = cfg.gene_families_to_names_file
# create a set of alignments
alignments = store.Alignments()
# load the usearch output
file_handle = open(cfg.usearch_uniref50_file)
for line in file_handle:
if not re.search("^#", line):
data = line.strip().split(config.blast_delimiter)
referenceids = data[config.blast_reference_index].split("|")
queryid = data[config.blast_query_index]
identity = float(data[config.blast_identity_index])
alignments.add(referenceids[1], 1, queryid, identity,
referenceids[0])
file_handle.close()
# set the output format
config.output_format = "tsv"
# set the location of the file to write to as a temp file
file_out, gene_families_file = tempfile.mkstemp()
os.close(file_out)
config.genefamilies_file = gene_families_file
# create gene_scores instance
gene_scores = store.GeneScores()
# obtain the gene families
gene_families_file = families.gene_families(alignments, gene_scores, 1)
# check the gene families output is as expected
self.assertTrue(
filecmp.cmp(gene_families_file,
cfg.gene_familes_uniref50_with_names_file,
shallow=False))
# reset the mapping file
config.gene_family_name_mapping_file = original_gene_family_mapping_file
# delete the temp file
utils.remove_temp_file(gene_families_file)
def test_compute_gene_abundance_in_pathways_without_reactions_database(
self):
"""
Test the compute gene abundance function
Test the GeneScores add function
Test without a reactions database (the pathways database is composed of genes)
"""
gene_scores = store.GeneScores()
# Add gene scores for two bugs
reactions_in_pathways_present = {}
bug = "bug1"
gene_scores.add_single_score(bug, "gene1", 1)
gene_scores.add_single_score(bug, "gene2", 2)
gene_scores.add_single_score(bug, "gene4", 4)
reactions_in_pathways_present[bug] = ["gene1", "gene2"]
bug = "bug2"
# Test with different values of gene1 for each bug
gene_scores.add_single_score(bug, "gene1", 1.1)
gene_scores.add_single_score(bug, "gene7", 7)
gene_scores.add_single_score(bug, "gene6", 6)
reactions_in_pathways_present[bug] = ["gene6"]
reactions_database = None
gene_abundance_in_pathways, remaining_gene_abundance = modules.compute_gene_abundance_in_pathways(
gene_scores, reactions_database, reactions_in_pathways_present)
# Check the gene abundances in pathways are correct
self.assertEqual(gene_abundance_in_pathways["bug1"], 3)
self.assertEqual(gene_abundance_in_pathways["bug2"], 6)
# Check the gene abundances not in pathways are correct
self.assertEqual(remaining_gene_abundance["bug1"], 4)
self.assertAlmostEqual(remaining_gene_abundance["bug2"], 8.1)
def test_pathways_abundance_with_names(self):
"""
Test the pathways abundance computation (xipe and minpath are off)
Test the pathways print function
Test the pathways mapping to names
Test the unmapped and unintegrated values are printed
"""
# update the max decimals to allow for rounding
config.output_max_decimals = 7
# Load in the pathways databases
reactions_database = store.ReactionsDatabase(
config.pathways_database_part1)
pathways_database = store.PathwaysDatabase(
config.pathways_database_part2, reactions_database)
# Load in the gene scores from the file
# This file has the gene names included
gene_scores = store.GeneScores()
gene_scores.add_from_file(
cfg.larger_gene_families_uniref50_with_names_file)
# Turn off xipe and minpath
minpath_toggle_original = config.minpath_toggle
config.minpath_toggle = "off"
xipe_toggle_original = config.xipe_toggle
config.xipe_toggle = "off"
pathways_and_reactions_store = modules.identify_reactions_and_pathways(
gene_scores, reactions_database, pathways_database)
# set the locations to write as temp files
file_out, abundance_file = tempfile.mkstemp()
os.close(file_out)
config.pathabundance_file = abundance_file
file_out, coverage_file = tempfile.mkstemp()
os.close(file_out)
config.pathcoverage_file = coverage_file
unaligned_reads_count = 10
abundance_file, coverage_file = modules.compute_pathways_abundance_and_coverage(
gene_scores, reactions_database, pathways_and_reactions_store,
pathways_database, unaligned_reads_count)
# Reset xipe and minpath
config.minpath_toggle = minpath_toggle_original
config.xipe_toggle = xipe_toggle_original
# check the output is as expected
self.assertTrue(
filecmp.cmp(abundance_file,
cfg.demo_pathabundance_file,
shallow=False))
utils.remove_temp_file(abundance_file)
utils.remove_temp_file(coverage_file)
def test_GeneScores_add_from_file_bug_list(self):
"""
GeneScores class: Test add_from_file bug list
"""
gene_scores=store.GeneScores()
gene_scores.add_from_file(cfg.genetable_file)
# Test the bug list is as expected
self.assertEqual(sorted(cfg.genetable_file_bug_scores.keys()),sorted(gene_scores.bug_list()))
def test_Alignments_compute_gene_scores_double_gene_double_query_with_temp_alignment_file(
self):
"""
Test the compute_gene_scores function
Test two hits to gene with more than one hit per query
Test with the temp alignment file
"""
# create a set of hits
# bug, reference, reference_length, query, matches = hit
matches1 = 41.0
matches2 = 57.1
matches3 = 61.0
matches4 = 72.1
gene1_length = 2
gene2_length = 3
gene3_length = 4
# Create a set of alignments
alignments_store = store.Alignments(minimize_memory_use=True)
alignments_store.add("gene1", gene1_length, "query1", matches1, "bug1")
alignments_store.add("gene2", gene2_length, "query1", matches2, "bug1")
alignments_store.add("gene2", gene2_length, "query2", matches3, "bug1")
alignments_store.add("gene3", gene3_length, "query3", matches4, "bug1")
gene_scores_store = store.GeneScores()
# compute gene scores
alignments_store.convert_alignments_to_gene_scores(gene_scores_store)
# gene1
hit1_score = math.pow(matches1, config.match_power)
hit2_score = math.pow(matches2, config.match_power)
query1_sum = hit1_score + hit2_score
# convert lengths to per kb
gene2_length = gene2_length / 1000.0
# gene2
hit3_score = math.pow(matches3, config.match_power)
query2_sum = hit3_score
expected_gene_score = hit3_score / query2_sum / gene2_length + hit2_score / query1_sum / gene2_length
actual_gene_score = gene_scores_store.get_score("bug1", "gene2")
# delete the temp alignment file
alignments_store.delete_temp_alignments_file()
self.assertAlmostEqual(actual_gene_score,
expected_gene_score,
places=7)
def test_GeneScores_add_from_file_scores(self):
"""
GeneScores class: Test add_from_file scores
"""
gene_scores=store.GeneScores()
gene_scores.add_from_file(cfg.genetable_file)
# Test the scores for all bugs and genes
for bug in cfg.genetable_file_bug_scores:
self.assertDictEqual(cfg.genetable_file_bug_scores[bug],gene_scores.scores_for_bug(bug))
def test_GeneScores_add_from_file_id_mapping_bug_list(self):
"""
GeneScores class: Test add_from_file bug list with id mapping
"""
gene_scores = store.GeneScores()
gene_scores.add_from_file(
cfg.genetable_file, id_mapping_file=cfg.id_mapping_gene_table_file)
# Test the bug list is as expected
self.assertEqual(
sorted(cfg.genetable_file_bug_scores_id_mapping.keys()),
sorted(gene_scores.bug_list()))
def test_GeneScores_get_score(self):
"""
GeneScores class: Test get_score function
"""
gene_scores=store.GeneScores()
bug1_scores={"gene1":1,"gene2":2}
gene_scores.add(bug1_scores,"bug1")
bug2_scores={"gene1":1,"gene2":2}
gene_scores.add(bug2_scores,"bug2")
self.assertEqual(gene_scores.get_score("bug1","gene2"),2)
def test_GeneScores_add(self):
"""
GeneScores class: Test add function
"""
gene_scores=store.GeneScores()
bug1_scores={"gene1":1,"gene2":2}
gene_scores.add(bug1_scores,"bug1")
bug2_scores={"gene1":1,"gene2":2}
gene_scores.add(bug2_scores,"bug2")
self.assertEqual(gene_scores.count_genes_for_bug("bug1"),2)
def test_compute_gene_abundance_in_pathways_with_reactions_database(self):
"""
Test the compute gene abundance function
Test the GeneScores add function
Test the ReactionsDatabase add function
Test with a reactions database (the pathways database is composed of reactions
and these reactions map to genes, with some genes mapping to multiple reactions)
"""
gene_scores = store.GeneScores()
# Add gene scores for two bugs
reactions_in_pathways_present = {}
bug = "bug1"
gene_scores.add_single_score(bug, "gene1", 1)
gene_scores.add_single_score(bug, "gene2", 2)
gene_scores.add_single_score(bug, "gene4", 4)
bug = "bug2"
# Test with different values of gene1 for each bug
gene_scores.add_single_score(bug, "gene1", 1.1)
gene_scores.add_single_score(bug, "gene7", 7)
gene_scores.add_single_score(bug, "gene6", 6)
gene_scores.add_single_score(bug, "gene8", 0.2)
reactions_database = store.ReactionsDatabase()
reactions = {
"reaction1": ["gene1", "gene6"],
"reaction2": ["gene1", "gene2"],
"reaction3": ["gene4", "gene7"],
"reaction4": ["gene8"]
}
reactions_database.add_reactions(reactions)
# Test one bug with two reactions and one bug with a single reaction
# For the bug with two reactions, test with both reactions including
# The same gene (to test this value is not added twice in the abundance result)
reactions_in_pathways_present["bug1"] = ["reaction1", "reaction2"]
reactions_in_pathways_present["bug2"] = ["reaction1"]
gene_abundance_in_pathways, remaining_gene_abundance = modules.compute_gene_abundance_in_pathways(
gene_scores, reactions_database, reactions_in_pathways_present)
# Check the gene abundances in pathways are correct
self.assertEqual(gene_abundance_in_pathways["bug1"], 3)
self.assertAlmostEqual(gene_abundance_in_pathways["bug2"], 7.1)
# Check the gene abundances not in pathways are correct
self.assertEqual(remaining_gene_abundance["bug1"], 4)
self.assertAlmostEqual(remaining_gene_abundance["bug2"], 7.2)
def test_GeneScores_add_second_set(self):
"""
GeneScores class: Test add function
Test adding a second set of scores to bug set
"""
gene_scores=store.GeneScores()
bug1_scores={"gene1":1,"gene2":2}
gene_scores.add(bug1_scores,"bug1")
bug1_scores_2={"gene3":1,"gene4":2, "gene2":22}
gene_scores.add(bug1_scores_2,"bug1")
self.assertEqual(gene_scores.count_genes_for_bug("bug1"),4)
def test_GeneScores_scores_for_bug(self):
"""
GeneScores class: Test scores_for_bug
"""
gene_scores=store.GeneScores()
bug1_scores={"gene1":1,"gene2":2}
gene_scores.add(bug1_scores,"bug1")
bug1_scores_2={"gene3":1,"gene4":2, "gene2":22}
gene_scores.add(bug1_scores_2,"bug1")
# Test that the most recent score for gene2 is returned
self.assertDictEqual(gene_scores.scores_for_bug("bug1"),
{"gene1":1,"gene2":22,"gene3":1,"gene4":2})
def test_GeneScores_get_score_second_set(self):
"""
GeneScores class: Test get_score function
Test getting the score for a second set of scores added to bug set
"""
gene_scores=store.GeneScores()
bug1_scores={"gene1":1,"gene2":2}
gene_scores.add(bug1_scores,"bug1")
bug1_scores_2={"gene3":1,"gene4":2, "gene2":22}
gene_scores.add(bug1_scores_2,"bug1")
# Test that the most recent score for gene2 is returned
self.assertEqual(gene_scores.get_score("bug1","gene2"),22)
def test_GeneScores_add_from_file_gene_list(self):
"""
GeneScores class: Test add_from_file gene list
"""
gene_scores=store.GeneScores()
gene_scores.add_from_file(cfg.genetable_file)
# Create a list of all of the genes in the table
genes={}
for bug in cfg.genetable_file_bug_scores:
for gene in cfg.genetable_file_bug_scores[bug]:
genes[gene]=1
# Test the gene list is as expected
self.assertEqual(sorted(genes.keys()),sorted(gene_scores.gene_list()))
def test_Alignments_compute_gene_scores_single_gene_single_query_with_temp_alignment_file(
self):
"""
Test the compute_gene_scores function
Test one hit for gene with one hit for query
Test with the temp alignment file
"""
# create a set of hits
matches1 = 41.0
matches2 = 57.1
matches3 = 61.0
matches4 = 72.1
gene1_length = 2
gene2_length = 3
gene3_length = 4
# Create a set of alignments
alignments_store = store.Alignments(minimize_memory_use=True)
alignments_store.add("gene1", gene1_length, "query1", matches1, "bug1")
alignments_store.add("gene2", gene2_length, "query1", matches2, "bug1")
alignments_store.add("gene2", gene2_length, "query2", matches3, "bug1")
alignments_store.add("gene3", gene3_length, "query3", matches4, "bug1")
gene_scores_store = store.GeneScores()
# compute gene scores
alignments_store.convert_alignments_to_gene_scores(gene_scores_store)
# convert lengths to per kb
gene3_length = gene3_length / 1000.0
# gene3
hit4_score = math.pow(matches4, config.match_power)
query3_sum = hit4_score
expected_gene_score = hit4_score / query3_sum / gene3_length
actual_gene_score = gene_scores_store.get_score("bug1", "gene3")
# delete the temp alignment file
alignments_store.delete_temp_alignments_file()
self.assertEqual(actual_gene_score, expected_gene_score)
def test_Alignments_compute_gene_scores_single_gene_double_query(self):
"""
Test the compute_gene_scores function
Test one hit for gene with more than one hit per query
"""
# create a set of hits
# bug, reference, reference_length, query, matches = hit
matches1 = 41.0
matches2 = 57.1
matches3 = 61.0
matches4 = 72.1
gene1_length = 2
gene2_length = 3
gene3_length = 4
# Create a set of alignments
alignments_store = store.Alignments()
alignments_store.add("gene1", gene1_length, "query1", matches1, "bug1")
alignments_store.add("gene2", gene2_length, "query1", matches2, "bug1")
alignments_store.add("gene2", gene2_length, "query2", matches3, "bug1")
alignments_store.add("gene3", gene3_length, "query3", matches4, "bug1")
gene_scores_store = store.GeneScores()
# compute gene scores
alignments_store.convert_alignments_to_gene_scores(gene_scores_store)
# convert lengths to per kb
gene1_length = gene1_length / 1000.0
# gene1
hit1_score = math.pow(matches1, config.match_power)
hit2_score = math.pow(matches2, config.match_power)
query1_sum = hit1_score + hit2_score
gene_score = hit1_score / query1_sum / gene1_length
self.assertEqual(gene_scores_store.get_score("bug1", "gene1"),
gene_score)
