def test_get_next_from_file(self):
'''get_next_from_file() should read seqs from OK, and raise error at badly formatted file'''
bad_files = [
'sequences_test_fail_no_AT.fq', 'sequences_test_fail_no_seq.fq',
'sequences_test_fail_no_plus.fq', 'sequences_test_fail_no_qual.fq'
]
bad_files = [os.path.join(data_dir, x) for x in bad_files]
for fname in bad_files:
f_in = utils.open_file_read(fname)
fq = sequences.Fastq()
with self.assertRaises(sequences.Error):
while fq.get_next_from_file(f_in):
pass
utils.close(f_in)
fname = os.path.join(data_dir, 'sequences_test_good_file.fq')
try:
f_in = open(fname)
except IOError:
print("Error opening '" + fname + "'", file=sys.stderr)
sys.exit(1)
fq = sequences.Fastq()
while fq.get_next_from_file(f_in):
self.assertEqual(fq, sequences.Fastq('ID', 'ACGTA', 'IIIII'))
utils.close(f_in)
def test_translate(self):
'''Test nucleatide -> amino acid conversion works on Fasta'''
fq = sequences.Fastq(
'ID',
'GCAGCCGCGGCTAGAAGGCGACGCCGGCGTAACAATGACGATTGCTGTGAAGAGCAACAGGGAGGCGGGGGTCACCATATAATCATTTTATTGCTACTCCTGCTTAAAAAGATGTTCTTTCCACCCCCGCCTAGCAGTTCATCCTCGTCTACAACCACGACTTGGTACTATGTAGTCGTGGTTTAATAGTGA',
'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'
)
self.assertEqual(
sequences.Fastq(
'ID',
'AAAARRRRRRNNDDCCEEQQGGGGHHIIILLLLLLKKMFFPPPPSSSSSSTTTTWYYVVVV***',
'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'
), fq.translate())
def test_to_Fastq(self):
'''Check to_Fastq converts OK, including out of range quality scores'''
fa = sequences.Fasta('X', 'AAAAA')
quals = [-1, 0, 40, 93, 94]
self.assertEqual(sequences.Fastq('X', 'AAAAA', '!!I~~'),
fa.to_Fastq(quals))
with self.assertRaises(sequences.Error):
fa.to_Fastq('AAAAAAAAAAAAA')
def test_trim(self):
'''trim() should trim the right number of bases off start and end'''
fq = sequences.Fastq('ID', '1234567890', '1234567890')
fq.trim(0, 0)
self.assertEqual(fq, sequences.Fastq('ID', '1234567890', '1234567890'))
fq = sequences.Fastq('ID', '1234567890', '1234567890')
fq.trim(1, 0)
self.assertEqual(fq, sequences.Fastq('ID', '234567890', '234567890'))
fq = sequences.Fastq('ID', '1234567890', '1234567890')
fq.trim(0, 1)
self.assertEqual(fq, sequences.Fastq('ID', '123456789', '123456789'))
fq = sequences.Fastq('ID', '1234567890', '1234567890')
fq.trim(2, 2)
self.assertEqual(fq, sequences.Fastq('ID', '345678', '345678'))
def test_trim_Ns(self):
'''trim_Ns() should do the right trimming of a fastq sequence'''
fq = sequences.Fastq('ID', 'ANNANA', '111111')
test_seqs = [
sequences.Fastq('ID', 'ANNANA', '111111'),
sequences.Fastq('ID', 'NANNANA', '1111111'),
sequences.Fastq('ID', 'NANNANAN', '11111111'),
sequences.Fastq('ID', 'ANNANAN', '1111111'),
sequences.Fastq('ID', 'NNNNNNANNANAN', '1111111111111'),
sequences.Fastq('ID', 'NNANNANANn', '1111111111')
]
for s in test_seqs:
s.trim_Ns()
self.assertEqual(fq, s)
def merge_to_one_seq(infile, outfile, seqname='union'):
'''Takes a multi fasta or fastq file and writes a new file that contains just one sequence, with the original sequences catted together, preserving their order'''
seq_reader = sequences.file_reader(infile)
seqs = []
for seq in seq_reader:
seqs.append(copy.copy(seq))
new_seq = ''.join([seq.seq for seq in seqs])
if type(seqs[0]) == sequences.Fastq:
new_qual = ''.join([seq.qual for seq in seqs])
seqs[:] = []
merged = sequences.Fastq(seqname, new_seq, new_qual)
else:
merged = sequences.Fasta(seqname, new_seq)
seqs[:] = []
f = utils.open_file_write(outfile)
print(merged, file=f)
utils.close(f)
def test_replace_interval(self):
'''Test replace_interval()'''
fa = sequences.Fasta('ID', 'ACGTA')
fa.replace_interval(0, 0, 'NEW')
self.assertEqual(fa, sequences.Fasta('ID', 'NEWCGTA'))
fa = sequences.Fasta('ID', 'ACGTA')
fa.replace_interval(4, 4, 'NEW')
self.assertEqual(fa, sequences.Fasta('ID', 'ACGTNEW'))
fa = sequences.Fasta('ID', 'ACGTA')
fa.replace_interval(2, 3, 'NEW')
self.assertEqual(fa, sequences.Fasta('ID', 'ACNEWA'))
fa = sequences.Fasta('ID', 'ACGTA')
with self.assertRaises(sequences.Error):
fa.replace_interval(3, 2, 'x')
with self.assertRaises(sequences.Error):
fa.replace_interval(1, 5, 'x')
with self.assertRaises(sequences.Error):
fa.replace_interval(5, 10, 'x')
fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE')
fq.replace_interval(0, 0, 'NEW', 'III')
self.assertEqual(fq, sequences.Fastq('ID', 'NEWCGTA', 'IIIBCDE'))
fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE')
fq.replace_interval(4, 4, 'NEW', 'III')
self.assertEqual(fq, sequences.Fastq('ID', 'ACGTNEW', 'ABCDIII'))
fq = sequences.Fastq('ID', 'ACGTA', 'ABCDE')
fq.replace_interval(2, 3, 'NEW', 'III')
self.assertEqual(fq, sequences.Fastq('ID', 'ACNEWA', 'ABIIIE'))
with self.assertRaises(sequences.Error):
fq.replace_interval(1, 1, 'x', 'xx')
def test_file_reader_fastq(self):
'''file_reader should iterate through a fastq file correctly'''
reader = sequences.file_reader(
os.path.join(data_dir, 'sequences_test_good_file.fq'))
for seq in reader:
self.assertEqual(seq, sequences.Fastq('ID', 'ACGTA', 'IIIII'))
def test_to_Fasta_and_qual(self):
'''Check to_Fasta_and_qual converts quality scores correctly'''
fq = sequences.Fastq('ID', 'ACGT', '>ADI')
(fa, qual) = fq.to_Fasta_and_qual()
self.assertEqual(fa, sequences.Fasta('ID', 'ACGT'))
self.assertListEqual(qual, [29, 32, 35, 40])
def test_revcomp(self):
'''revcomp() should correctly reverse complement a sequence'''
fq = sequences.Fastq('ID', 'ACGTNacgtn', '1234567890')
fq.revcomp()
self.assertEqual(fq, sequences.Fastq('ID', 'nacgtNACGT', '0987654321'))
def test_init_length_mismatch(self):
'''__init__ should raise an error when length of seq and quality not the same'''
with self.assertRaises(sequences.Error):
sequences.Fastq('X', 'A', 'II')
def setUp(self):
self.fastq = sequences.Fastq('ID', 'ACGTA', 'IIIII')
def test_expand_nucleotides(self):
'''Test expand_nucleotides'''
tests = [
(sequences.Fasta('1', 'A'), [sequences.Fasta('1.1', 'A')]),
(sequences.Fasta('2', 'C'), [sequences.Fasta('2.1', 'C')]),
(sequences.Fasta('3', 'G'), [sequences.Fasta('3.1', 'G')]),
(sequences.Fasta('4', 'T'), [sequences.Fasta('4.1', 'T')]),
(sequences.Fasta('6', 'R'),
[sequences.Fasta('6.1', 'A'),
sequences.Fasta('6.2', 'G')]),
(sequences.Fasta('7', 'Y'),
[sequences.Fasta('7.1', 'C'),
sequences.Fasta('7.2', 'T')]),
(sequences.Fasta('8', 'S'),
[sequences.Fasta('8.1', 'C'),
sequences.Fasta('8.2', 'G')]),
(sequences.Fasta('9', 'W'),
[sequences.Fasta('9.1', 'A'),
sequences.Fasta('9.2', 'T')]),
(sequences.Fasta('10', 'K'),
[sequences.Fasta('10.1', 'G'),
sequences.Fasta('10.2', 'T')]),
(sequences.Fasta('11', 'M'),
[sequences.Fasta('11.1', 'A'),
sequences.Fasta('11.2', 'C')]),
(sequences.Fasta('12', 'B'), [
sequences.Fasta('12.1', 'C'),
sequences.Fasta('12.2', 'G'),
sequences.Fasta('12.3', 'T')
]),
(sequences.Fasta('13', 'D'), [
sequences.Fasta('13.1', 'A'),
sequences.Fasta('13.2', 'G'),
sequences.Fasta('13.3', 'T')
]),
(sequences.Fasta('14', 'H'), [
sequences.Fasta('14.1', 'A'),
sequences.Fasta('14.2', 'C'),
sequences.Fasta('14.3', 'T')
]),
(sequences.Fasta('15', 'V'), [
sequences.Fasta('15.1', 'A'),
sequences.Fasta('15.2', 'C'),
sequences.Fasta('15.3', 'G')
]),
(sequences.Fasta('16', 'N'), [
sequences.Fasta('16.1', 'A'),
sequences.Fasta('16.2', 'C'),
sequences.Fasta('16.3', 'G'),
sequences.Fasta('16.4', 'T')
]),
(sequences.Fasta('17', 'ART'),
[sequences.Fasta('17.1', 'AAT'),
sequences.Fasta('17.2', 'AGT')]),
(sequences.Fasta('18', 'ARRT'), [
sequences.Fasta('18.1', 'AAAT'),
sequences.Fasta('18.2', 'AAGT'),
sequences.Fasta('18.3', 'AGAT'),
sequences.Fasta('18.4', 'AGGT')
]),
(sequences.Fasta('19', 'ARTR'), [
sequences.Fasta('19.1', 'AATA'),
sequences.Fasta('19.2', 'AATG'),
sequences.Fasta('19.3', 'AGTA'),
sequences.Fasta('19.4', 'AGTG')
]),
(sequences.Fastq('20', 'ART', 'GHI'), [
sequences.Fastq('20.1', 'AAT', 'GHI'),
sequences.Fastq('20.2', 'AGT', 'GHI')
]),
]
for t in tests:
self.assertListEqual(t[0].expand_nucleotides(), t[1])