def test_translated_search_unaligned_reads_annotations_gene_length(self):
"""
Test the unaligned reads and the store alignments
Test with a rapsearch2 output file
Test the different annotation formats are recognized for gene length
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# load the rapsearch2 output with the unaligned reads function
unaligned_file_fasta=translated_search.unaligned_reads(unaligned_reads_store,
cfg.rapsearch_file_annotations, alignments)
# remove temp file
utils.remove_temp_file(unaligned_file_fasta)
# 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
for hit in all_hits:
query, bug, reference, evalue, length = hit
if reference == "UniRef50":
self.assertEqual(length,2000)
else:
self.assertEqual(length,1000)
def test_Read_print_fasta_id_count(self):
"""
Read class: Test the loading of a full fasta file
Test the total number of expected ids are loaded
"""
reads_store=store.Reads(cfg.small_fasta_file)
# Check that the total number of expected reads are loaded
self.assertEqual(len(reads_store.id_list()), cfg.small_fasta_file_total_sequences)
def test_Read_delete_id(self):
"""
Read class: Test the deleting of ids
"""
reads_store=store.Reads(cfg.small_fasta_file)
# delete all of the reads and check structure is empty
for id in reads_store.id_list():
reads_store.remove_id(id)
self.assertEqual(len(reads_store.id_list()), 0)
def test_translated_search_unaligned_reads_annotations_bug(self):
"""
Test the unaligned reads and the store alignments
Test with a rapsearch2 output file
Test the different annotation formats are recognized for bug
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# load the rapsearch2 output with the unaligned reads function
unaligned_file_fasta=translated_search.unaligned_reads(unaligned_reads_store,
cfg.rapsearch_file_annotations, alignments)
# remove temp file
utils.remove_temp_file(unaligned_file_fasta)
# there should be one bug name and the other should be unclassified
self.assertEqual(sorted(alignments.bug_list()),sorted(["s__Bacteroides_xylanisolvens","unclassified"]))
def test_Read_print_fasta_id_list(self):
"""
Read class: Test the loading of a full fasta file
Test the expected ids are loaded
"""
reads_store=store.Reads(cfg.small_fasta_file)
# Check the reads are printed correctly
printed_stored_fasta=reads_store.get_fasta()
compare_fasta={}
# organize the fasta from the read class and the
# file of correct fasta output
file_handle=open(cfg.small_fasta_file_single_line_sequences)
for input in [printed_stored_fasta.split("\n"), file_handle]:
id=""
seq=""
for line in input:
if re.search(">",line):
# store prior id
if id and seq:
compare_fasta[id]=compare_fasta.get(id,[])+[seq]
id=line.strip()
seq=""
else:
seq=line.strip()
# store the last sequence found
if id and seq:
compare_fasta[id]=compare_fasta.get(id,[])+[seq]
file_handle.close()
# check there are still the same number of ids
self.assertEqual(len(compare_fasta.keys()),cfg.small_fasta_file_total_sequences)
# check the sequences match
for id, sequences in compare_fasta.items():
self.assertTrue(len(sequences)==2)
self.assertEqual(sequences[0], sequences[1])
def test_translated_search_unaligned_reads_annotations_reference(self):
"""
Test the unaligned reads and the store alignments
Test with a rapsearch2 output file
Test the different annotation formats are recognized for reference
"""
# create a set of alignments
alignments=store.Alignments()
unaligned_reads_store=store.Reads()
# load the rapsearch2 output with the unaligned reads function
unaligned_file_fasta=translated_search.unaligned_reads(unaligned_reads_store,
cfg.rapsearch_file_annotations, alignments)
# remove temp file
utils.remove_temp_file(unaligned_file_fasta)
# three of the hits should be for gene "UniRef50"
hits=alignments.hits_for_gene("UniRef50")
self.assertEqual(len(hits),3)
def test_translated_search_unaligned_reads_rapsearch_log(self):
"""
Test the unaligned reads function
Test with a rapsearch output file
Test that log of evalue is taken
"""
# create a set of alignments
alignments=store.Alignments()
# load the rapsearch output
file_handle=open(cfg.rapsearch2_output_file_with_header)
for line in file_handle:
if not re.search("^#",line):
data=line.strip().split(config.blast_delimiter)
referenceid=data[config.blast_reference_index]
queryid=data[config.blast_query_index]
evalue=float(data[config.blast_evalue_index])
alignments.add(referenceid, 0, queryid, evalue,"unclassified")
file_handle.close()
alignments_test=store.Alignments()
unaligned_reads_store=store.Reads()
# load the rapsearch output with the unaligned reads function
unaligned_file_fasta=translated_search.unaligned_reads(unaligned_reads_store,
cfg.rapsearch2_output_file_with_header, alignments_test)
# remove temp file
utils.remove_temp_file(unaligned_file_fasta)
# check the evalues are changed
hit1_evalue=sorted(alignments.get_hit_list())[0][-2]
hit1_evalue_test=sorted(alignments_test.get_hit_list())[0][-2]
self.assertAlmostEqual(math.pow(10.0,math.log(hit1_evalue)*-1),
math.log(hit1_evalue_test)*-1,places=7)
def test_translated_search_unaligned_reads_blastm8(self):
"""
Test the unaligned reads and the store alignments
Test with a blastm8-like output file
Test with empty reads structure
Test that log of evalue is not taken
Test that function does not require gene lengths in reference id
"""
# create a set of alignments
alignments=store.Alignments()
# load the blastm8-like output
file_handle=open(cfg.rapsearch2_output_file_without_header)
for line in file_handle:
if not re.search("^#",line):
data=line.strip().split(config.blast_delimiter)
referenceid=data[config.blast_reference_index]
queryid=data[config.blast_query_index]
evalue=float(data[config.blast_evalue_index])
alignments.add(referenceid, 0, queryid, evalue,"unclassified")
file_handle.close()
alignments_test=store.Alignments()
unaligned_reads_store=store.Reads()
# load the blastm8-like output with the unaligned reads function
unaligned_file_fasta=translated_search.unaligned_reads(unaligned_reads_store,
cfg.rapsearch2_output_file_without_header, alignments_test)
# remove temp file
utils.remove_temp_file(unaligned_file_fasta)
# check the evalues are unchanged
self.assertEqual(sorted(alignments.get_hit_list()), sorted(alignments_test.get_hit_list()))