def test_sort_by_position_in_ref(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
# with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
# it fails because bwa somehow gives a position to an unmapped seq
# with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
# sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand],
key='seq',
directory=None,
max_items_in_memory=None,
tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
def test_sort_by_position_in_ref(self):
reference = GENOME
ref_fhand = NamedTemporaryFile()
ref_fhand.write(reference)
ref_fhand.flush()
#with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files([in_fhand], 'coordinate', ref_fhand.name):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files([in_fhand], 'coordinate', ref_fhand.name):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand], key='seq', directory=None,
max_items_in_memory=None, tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
def test_sort_by_position_in_ref(self):
index_fpath = os.path.join(TEST_DATA_DIR, 'ref_example.fasta')
#with fasta format
query1 = '>seq1\nGAGAATTAAGCCTATCTGGAGAGCGGTACCAACAGGGAAACACCGACTCA\n'
query2 = '>seq2\nTAACAGTATGTGCCGTAGGGCCGTCGCCGCATCCACGTTATCGGAAGGGC\n'
query3 = '>seq3\nTACGGCCGTCCCCCTGCTGCTTATCATCAGGCGACGATAGTCAGCTCCGC\n'
query4 = '>seq4\nTGCAGAGACCGACATGCGAAAGGAGTGACTATCACCGTCAATGGCGTGCC\n'
query5 = '>seq5\nAATAAATAATCTGGGTATGTACTCGGAGTCTACGTAAGCGCGCTTAAATT\n'
query6 = '>seq6\nAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#it fails because bwa somehow gives a position to an unmapped seq
#with fastq format
query1 += '+\n??????????????????????????????????????????????????\n'
query2 += '+\n??????????????????????????????????????????????????\n'
query3 += '+\n??????????????????????????????????????????????????\n'
query4 += '+\n??????????????????????????????????????????????????\n'
query5 += '+\n??????????????????????????????????????????????????\n'
query6 += '+\n??????????????????????????????????????????????????\n'
query = query6 + query1 + query2 + query3 + query4 + query5
in_fhand = NamedTemporaryFile()
in_fhand.write(query)
in_fhand.flush()
sorted_names = []
for seq in sort_fastx_files(in_fhand, 'coordinate', index_fpath):
sorted_names.append(get_name(seq))
expected_names = ['seq2', 'seq3', 'seq1', 'seq5', 'seq4', 'seq6']
assert sorted_names == expected_names
#sort by sequence
sorted_names = []
for seq in sort_fastx_files([in_fhand], key='seq', directory=None,
max_items_in_memory=None, tempdir=None):
sorted_names.append(get_name(seq))
expected_names = ['seq6', 'seq5', 'seq1', 'seq2', 'seq3', 'seq4']
assert sorted_names == expected_names
