def test_nucleotide_search_unaligned_reads_read_count_aligned_subject_coverage(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test for aligned read counts
Test with subject coverage filtering
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off subject filtering
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_unaligned_reads, alignments, unaligned_reads_store, keep_sam=True)
# reset subject filtering
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# check the aligned reads count
self.assertEqual(len(alignments.get_hit_list()),cfg.sam_file_unaligned_reads_total_aligned_subject_coverage)
def test_nucleotide_search_unaligned_reads_output_fasta_format(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test output file is of fasta format
Test sam file is not removed
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_unaligned_reads, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# check for fasta output file format
file_format=utilities.determine_file_format(unaligned_reads_file_fasta)
self.assertEqual("fasta",file_format)
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
def test_nucleotide_search_unaligned_reads_output_blast_format(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test the aligned reads file created is of the blastm8 format
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
config.file_basename="TEST"
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_annotations, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# test file is of the blastm8 format
file_format=utilities.determine_file_format(reduced_aligned_reads_file)
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
self.assertEqual(file_format,"blastm8")
def test_nucleotide_search_unaligned_reads_annotations_bug(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test the different annotation formats are recognized for bug
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_annotations, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# there should be one bug which is unclassified
self.assertEqual(alignments.bug_list(),["unclassified"])
def test_nucleotide_search_unaligned_reads_annotations_reference(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test the different annotation formats are recognized for reference
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_annotations, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# two of the hits should be for gene "UniRef50"
hits=alignments.hits_for_gene("UniRef50")
self.assertEqual(len(hits),2)
def test_nucleotide_search_unaligned_reads_read_count_unaligned_minimize_memory_use(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test for unaligned read counts
Test with minimize memory use
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads(minimize_memory_use=True)
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_unaligned_reads, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# check the unaligned reads count
self.assertEqual(unaligned_reads_store.count_reads(),cfg.sam_file_unaligned_reads_total_unaligned)
def test_nucleotide_search_unaligned_reads_annotations_gene_length(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test the different annotation formats are recognized for gene length
Test the gene length uses the read length from the sam file
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_annotations, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# there should be 4 hits identified
all_hits=alignments.get_hit_list()
self.assertEqual(len(all_hits),4)
# check for set and default gene lengths
read_length = 151
expected_length_uniref50 = (abs(2000 - read_length)+1)/1000.0
expected_length_other = (abs(1000 - read_length)+1)/1000.0
for hit in all_hits:
query, bug, reference, score, length = hit
if reference == "UniRef50":
self.assertEqual(length,expected_length_uniref50)
else:
self.assertEqual(length,expected_length_other)
def test_nucleotide_search_unaligned_reads_read_count_aligned_evalue_threshold(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test for aligned read counts
Test the evalue threshold does not filter alignments
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# update the evalue threshold to a number less than those for the alignment file
original_evalue_threshold=config.evalue_threshold
config.evalue_threshold=1e-15
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_unaligned_reads, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# reset the evalue threshold back to the original
config.evalue_threshold=original_evalue_threshold
# check the aligned reads count (all reads should be aligned even though they do not
# meet the threshold as the evalue threshold is not applied for this type of alignment)
self.assertEqual(len(alignments.get_hit_list()),cfg.sam_file_unaligned_reads_total_aligned)
def test_nucleotide_search_unaligned_reads_read_count_aligned_identity_threshold(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test for aligned read counts
Test the identity threshold does filter alignments
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# update the identity threshold to a number larger than those in the alignments
original_identity_threshold=config.identity_threshold
config.identity_threshold=101.0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_unaligned_reads, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# reset the identity threshold back to the original
config.identity_threshold=original_identity_threshold
# check the aligned reads count (it should be two as both should pass the threshold)
self.assertEqual(len(alignments.get_hit_list()),2)
def test_nucleotide_search_unaligned_reads_scores(self):
"""
Test the unaligned reads and the store alignments
Test with a bowtie2/sam output file
Test the scores are based on percent identities
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# turn off query/subject filtering
config.nucleotide_subject_coverage_threshold = 0
config.nucleotide_query_coverage_threshold = 0
# read in the aligned and unaligned reads
[unaligned_reads_file_fasta, reduced_aligned_reads_file] = nucleotide.unaligned_reads(
cfg.sam_file_annotations, alignments, unaligned_reads_store, keep_sam=True)
# reset query/subject filtering
config.nucleotide_subject_coverage_threshold = self.default_nucleotide_subject_coverage_threshold
config.nucleotide_query_coverage_threshold = self.default_nucleotide_query_coverage_threshold
# remove temp files
utils.remove_temp_file(unaligned_reads_file_fasta)
utils.remove_temp_file(reduced_aligned_reads_file)
# there should be 4 hits identified
all_hits=alignments.get_hit_list()
# check for set and default gene lengths
expected_score=math.pow(151.0, config.match_power)
for hit in all_hits:
query, bug, reference, score, length = hit
self.assertEqual(score,expected_score)
