def test_file_to_dict(self):
'''check file_to_dict fills dictionary correctly'''
d_test = {}
d = {}
tasks.file_to_dict(os.path.join(data_dir, 'sequences_test.fa'), d_test)
for i in range(1, 5):
d[str(i)] = sequences.Fasta(str(i), 'ACGTA')
self.assertSequenceEqual(d_test.keys(), d.keys())
for i in range(1, 5):
key = str(i)
self.assertEqual(d_test[key].id, d[key].id)
self.assertEqual(d_test[key].seq, d[key].seq)
def deinterleave(infile, outfile_1, outfile_2, fasta_out=False):
seq_reader = sequences.file_reader(infile)
f_1 = utils.open_file_write(outfile_1)
f_2 = utils.open_file_write(outfile_2)
for seq in seq_reader:
if fasta_out:
print(sequences.Fasta(seq.id, seq.seq), file=f_1)
else:
print(seq, file=f_1)
try:
next(seq_reader)
except StopIteration:
utils.close(f_1)
utils.close(f_2)
raise Error('Error getting mate for sequence. Cannot continue')
if fasta_out:
print(sequences.Fasta(seq.id, seq.seq), file=f_2)
else:
print(seq, file=f_2)
utils.close(f_1)
utils.close(f_2)
def test_get_next_from_embl_file(self):
f_in = utils.open_file_read(
os.path.join(data_dir, 'sequences_test.embl'))
embl = sequences.Embl()
counter = 1
while embl.get_next_from_file(f_in):
self.assertEqual(
embl,
sequences.Fasta('seq' + str(counter),
expected_embl[counter - 1]))
counter += 1
utils.close(f_in)
def test_trim_Ns(self):
'''trim_Ns() should do the right trimming of a sequence'''
fa = sequences.Fasta('ID', 'ANNANA')
test_seqs = [sequences.Fasta('ID', 'ANNANA'),
sequences.Fasta('ID', 'NANNANA'),
sequences.Fasta('ID', 'NANNANAN'),
sequences.Fasta('ID', 'ANNANAN'),
sequences.Fasta('ID', 'NNNNNNANNANAN'),
sequences.Fasta('ID', 'NNANNANANn')]
for s in test_seqs:
s.trim_Ns()
self.assertEqual(fa, s)
def test_file_reader_phylip(self):
'''Test read phylip file'''
test_files = [
'sequences_test_phylip.interleaved',
'sequences_test_phylip.interleaved2',
'sequences_test_phylip.sequential'
]
test_files = [os.path.join(data_dir, f) for f in test_files]
expected_seqs = [
sequences.Fasta('Turkey', 'AACTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT'),
sequences.Fasta('Salmo_gair', 'AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT'),
sequences.Fasta('H. Sapiens', 'ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA')
]
for fname in test_files:
reader = sequences.file_reader(fname)
i = 0
for seq in reader:
self.assertEqual(expected_seqs[i], seq)
i += 1
# files made by seaview are a little different in the first line.
# Test one of these
expected_seqs = [
sequences.Fasta('seq1', 96 * 'G' + 'T'),
sequences.Fasta('seq2', 94 * 'A' + 'G')
]
reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test_phylip.made_by_seaview'))
i = 0
for seq in reader:
print(seq)
self.assertEqual(expected_seqs[i], seq)
i += 1
def test_is_complete_orf(self):
'''Test is_complete_orf'''
tests = [
(sequences.Fasta('ID', 'TTT'), False),
(sequences.Fasta('ID', 'TTTTAA'), True),
(sequences.Fasta('ID', 'TTTTAATAA'), False),
(sequences.Fasta('ID', 'TTGTAA'), True),
(sequences.Fasta('ID', 'TTTAAC'), True),
(sequences.Fasta('ID', 'TGA'), False),
(sequences.Fasta('ID', 'TGAA'), False),
]
for t in tests:
self.assertEqual(t[0].is_complete_orf(), t[1])
def get_next_from_file(self, f):
self.__init__()
line = f.readline()
if not line:
return None
while line == '\n':
line = f.readline()
if not line.startswith('DNA : '):
raise Error("Error reading caf file. Expected line starting with 'DNA : ...'")
self.id = line.rstrip().split()[2]
line = f.readline()
seq = []
while line != '\n':
seq.append(line.rstrip())
line = f.readline()
self.seq = sequences.Fasta(self.id, ''.join(seq))
line = f.readline()
if not line.startswith('BaseQuality : '):
raise Error("Error reading caf file. Expected line starting with 'BaseQuality : ...'")
quals = [int(x) for x in f.readline().rstrip().split()]
self.seq = self.seq.to_Fastq(quals)
line = f.readline()
assert line == '\n'
line = f.readline()
while line not in ['', '\n']:
a = line.rstrip().split()
if a[0] == 'Insert_size':
self.insert_min, self.insert_max = int(a[1]), int(a[2])
elif a[0] == 'Ligation_no':
self.ligation = a[1]
elif a[0] == 'Clone':
self.clone = a[1]
elif a[0] == 'Clipping' and a[1] == 'QUAL':
self.clip_start, self.clip_end = int(a[2]) - 1, int(a[3]) - 1
line = f.readline()
return True
def test_get_next_from_gbk_file(self):
f_in = utils.open_file_read(
os.path.join(data_dir, 'sequences_test.gbk'))
embl = sequences.Embl()
counter = 1
expected = [
'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgatc',
'gatcctccatatacaacggtatctccacctcaggtttagatctcaacaacggaaccattgccgacatgagacagttaggtatcgtcgagagttacaagctaaaacgagcagtagtcagctctgcatctgaagccgctgaagttctactaagggtggataacatcatccgtgcaagaccaatgccatgactcagattctaattttaagctattcaatttctctttgaaa'
]
while embl.get_next_from_file(f_in):
self.assertEqual(
embl,
sequences.Fasta('NAME' + str(counter), expected[counter - 1]))
counter += 1
utils.close(f_in)
def test_looks_like_gene(self):
'''Test looks_like_gene'''
tests = [
(sequences.Fasta('ID', 'TTT'), False),
(sequences.Fasta('ID', 'TTGTAA'), True),
(sequences.Fasta('ID', 'ttgTAA'), True),
(sequences.Fasta('ID', 'TTGTTTTAA'), True),
(sequences.Fasta('ID', 'TTGTAATTTTAA'), False),
(sequences.Fasta('ID', 'TTGTTTTGAA'), False),
]
for t in tests:
self.assertEqual(t[0].looks_like_gene(), t[1])
sequences.genetic_code = 1
self.assertFalse(sequences.Fasta('ID', 'ATTCAGTAA').looks_like_gene())
sequences.genetic_code = 11
self.assertTrue(sequences.Fasta('ID', 'ATTCAGTAA').looks_like_gene())
sequences.genetic_code = 1
def test_gc_content(self):
"""Test GC content calculation works as expected"""
tests = [
(sequences.Fasta('ID', 'cgCG'), 1.0),
(sequences.Fasta('ID', 'tTaA'), 0.0),
(sequences.Fasta('ID', 'GCAT'), 0.5),
(sequences.Fasta('ID', 'GCATNN'), 0.5),
(sequences.Fasta('ID', 'GCATNNS'), 0.6),
(sequences.Fasta('ID', 'GCATNNSK'), 0.5)
]
for test, answer in tests:
self.assertAlmostEqual(test.gc_content(), answer)
self.assertAlmostEqual(test.gc_content(as_decimal=False), answer * 100)
def scaffolds_to_contigs(infile, outfile, number_contigs=False):
'''Makes a file of contigs from scaffolds by splitting at every N.
Use number_contigs=True to add .1, .2, etc onto end of each
contig, instead of default to append coordinates.'''
seq_reader = sequences.file_reader(infile)
fout = utils.open_file_write(outfile)
for seq in seq_reader:
contigs = seq.contig_coords()
counter = 1
for contig in contigs:
if number_contigs:
name = seq.id + '.' + str(counter)
counter += 1
else:
name = '.'.join([seq.id, str(contig.start + 1), str(contig.end + 1)])
print(sequences.Fasta(name, seq[contig.start:contig.end+1]), file=fout)
utils.close(fout)
def test_file_reader_embl(self):
'''Test read embl file'''
reader = sequences.file_reader(os.path.join(data_dir, 'sequences_test.embl'))
counter = 1
for seq in reader:
self.assertEqual(seq, sequences.Fasta('seq' + str(counter), expected_embl[counter-1]))
counter += 1
bad_files = [
'sequences_test.embl.bad',
'sequences_test.embl.bad2',
]
bad_files = [os.path.join(data_dir, x) for x in bad_files]
for filename in bad_files:
with self.assertRaises(sequences.Error):
reader = sequences.file_reader(filename)
for seq in reader:
pass
def make_random_contigs(contigs, length, outfile, name_by_letters=False, prefix='', seed=None, first_number=1):
'''Makes a multi fasta file of random sequences, all the same length'''
random.seed(a=seed)
fout = utils.open_file_write(outfile)
letters = list('ABCDEFGHIJKLMNOPQRSTUVWXYZ')
letters_index = 0
for i in range(contigs):
if name_by_letters:
name = letters[letters_index]
letters_index += 1
if letters_index == len(letters):
letters_index = 0
else:
name = str(i + first_number)
fa = sequences.Fasta(prefix + name, ''.join([random.choice('ACGT') for x in range(length)]))
print(fa, file=fout)
utils.close(fout)
def to_fasta(infile,
outfile,
line_length=60,
strip_after_first_whitespace=False):
seq_reader = sequences.file_reader(infile)
f_out = utils.open_file_write(outfile)
original_line_length = sequences.Fasta.line_length
sequences.Fasta.line_length = line_length
for seq in seq_reader:
if strip_after_first_whitespace:
seq.strip_after_first_whitespace()
if type(seq) == sequences.Fastq:
print(sequences.Fasta(seq.id, seq.seq), file=f_out)
else:
print(seq, file=f_out)
utils.close(f_out)
sequences.Fasta.line_length = original_line_length
def test_extend(self):
'''Test extend'''
ctg = contig.Contig(sequences.Fasta('ID', 'ACCGT'))
self.assertEqual(ctg.extend(5, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'ACCGT'))
ctg.add_left_kmer('GT')
self.assertEqual(ctg.extend(1, 2, 100), (2, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGT'))
self.assertEqual(ctg.extend(1, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGT'))
ctg.add_right_kmer('TG')
self.assertEqual(ctg.extend(1, 2, 100), (0, 2))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGTTG'))
self.assertEqual(ctg.extend(1, 2, 100), (0, 0))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'GTACCGTTG'))
ctg.add_left_kmer('AG')
ctg.add_right_kmer('GC')
self.assertEqual(ctg.extend(1, 2, 100), (2, 2))
self.assertEqual(ctg.fa, sequences.Fasta('ID', 'AGGTACCGTTGGC'))
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 to_fasta(infile,
outfile,
line_length=60,
strip_after_first_whitespace=False,
check_unique=False):
seq_reader = sequences.file_reader(infile)
f_out = utils.open_file_write(outfile)
original_line_length = sequences.Fasta.line_length
sequences.Fasta.line_length = line_length
if check_unique:
used_names = {}
for seq in seq_reader:
if strip_after_first_whitespace:
seq.strip_after_first_whitespace()
if check_unique:
used_names[seq.id] = used_names.get(seq.id, 0) + 1
if type(seq) == sequences.Fastq:
print(sequences.Fasta(seq.id, seq.seq), file=f_out)
else:
print(seq, file=f_out)
utils.close(f_out)
sequences.Fasta.line_length = original_line_length
if check_unique:
all_unique = True
for name, count in used_names.items():
if count > 1:
print('Sequence name "' + name + '" not unique. Found',
count,
'times',
file=sys.stderr)
all_unique = False
if not all_unique:
raise Error('Not all sequence names unique. Cannot continue')
def test_contig_coords(self):
'''contig_coords() should get the coords of all contigs in a sequence correctly'''
test_seqs = [sequences.Fasta('ID', 'ACGT'),
sequences.Fasta('ID', 'NACGT'),
sequences.Fasta('ID', 'NNACGT'),
sequences.Fasta('ID', 'ACGTN'),
sequences.Fasta('ID', 'ACGTNN'),
sequences.Fasta('ID', 'NANNCGT'),
sequences.Fasta('ID', 'ACNNNGTNA'),
sequences.Fasta('ID', 'ANNCGTNNAAAAA')]
correct_coords = [[intervals.Interval(0,3)],
[intervals.Interval(1, 4)],
[intervals.Interval(2, 5)],
[intervals.Interval(0, 3)],
[intervals.Interval(0, 3)],
[intervals.Interval(1, 1), intervals.Interval(4,6)],
[intervals.Interval(0, 1), intervals.Interval(5, 6), intervals.Interval(8, 8)],
[intervals.Interval(0, 0), intervals.Interval(3, 5), intervals.Interval(8, 12)]]
for i in range(len(test_seqs)):
gaps = test_seqs[i].contig_coords()
self.assertListEqual(correct_coords[i], gaps)
def test_strip_illumina_suffix(self):
'''Check that /1 and /2 removed correctly from IDs'''
seqs = [sequences.Fasta('name/1', 'A'),
sequences.Fasta('name/2', 'A'),
sequences.Fasta('name', 'A'),
sequences.Fasta('name/1/2', 'A'),
sequences.Fasta('name/2/1', 'A'),
sequences.Fasta('name/3', 'A')]
correct_names = ['name', 'name', 'name', 'name/1', 'name/2', 'name/3']
for seq in seqs:
seq.strip_illumina_suffix()
for i in range(len(seqs)):
self.assertEqual(seqs[i].id, correct_names[i])
def run(self): '''Produce a filtered fasta file.''' original_dir = os.getcwd() os.chdir(self.working_directory) small_contigs = set() contained_contigs = set() if len(self.contigs) > len(self.ids_to_skip): alignments = utils.run_nucmer(self.fasta_file, self.fasta_file, self._build_nucmer_filename(), min_percent_id=self.percent_match, run_promer=False) for id in self.contigs.keys(): if not id in self.ids_to_skip: if len(self.contigs[id]) < self.cutoff_contig_length: small_contigs.add(id) else: for algn in alignments: if (not algn.is_self_hit()) \ and algn.qry_name == id \ and algn.ref_name != algn.qry_name \ and not algn.ref_name in contained_contigs \ and (algn.hit_length_qry/algn.qry_length) * 100 >= self.percent_match: contained_contigs.add(id) discard = small_contigs.union(contained_contigs) ids_file = utils.write_ids_to_file(discard, "contig.ids.discard") tasks.filter(self.fasta_file, self.output_file, ids_file=ids_file, invert=True) if not self.debug: utils.delete(ids_file) utils.delete(self._build_nucmer_filename()) else: output_fw = fastaqutils.open_file_write(self.output_file) for contig_id in self.contigs: print(sequences.Fasta(contig_id, self.contigs[contig_id]), file=output_fw) fastaqutils.close(output_fw) self._write_summary(small_contigs, contained_contigs) os.chdir(original_dir)
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_add_insertions(self):
'''Test add_insertions'''
fa = sequences.Fasta('X', 'acgtacgtacgt')
fa.add_insertions(skip=4, window=0, test=True)
self.assertEqual(fa, sequences.Fasta('X', 'acgtNacgtNacgt'))
def run(description):
parser = argparse.ArgumentParser(
description = 'Makes perfect paired end fastq reads from a sequence file, with insert sizes sampled from a normal distribution. Read orientation is innies. Output is an interleaved FASTQ file.',
usage = 'fastaq to_perfect_reads [options] <infile> <outfile> <mean insert size> <insert std deviation> <mean coverage> <read length>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
parser.add_argument('mean_insert', type=int, help='Mean insert size of read pairs', metavar='mean insert size')
parser.add_argument('insert_std', type=float, help='Standard devation of insert size', metavar='insert std deviation')
parser.add_argument('coverage', type=float, help='Mean coverage of the reads', metavar='mean coverage')
parser.add_argument('readlength', type=int, help='Length of each read', metavar='read length')
parser.add_argument('--fragments', help='Write FASTA sequences of fragments (i.e. read pairs plus sequences in between them) to the given filename', metavar='FILENAME')
parser.add_argument('--no_n', action='store_true', help='Don\'t allow any N or n characters in the reads')
parser.add_argument('--seed', type=int, help='Seed for random number generator. Default is to use python\'s default', default=None, metavar='INT')
options = parser.parse_args()
random.seed(a=options.seed)
seq_reader = sequences.file_reader(options.infile)
fout = utils.open_file_write(options.outfile)
pair_counter = 1
if options.fragments:
fout_frags = utils.open_file_write(options.fragments)
for ref in seq_reader:
# check if current seq is long enough
if len(ref) < options.mean_insert + 4 * options.insert_std:
print('Warning, sequence ', ref.id, ' too short. Skipping it...', file=sys.stderr)
continue
# work out how many reads to simulate
read_pairs = int(0.5 * options.coverage * len(ref) / options.readlength)
# it's possible that we pick the same fragment twice, in which case the
# reads would get the same name. So remember the frag coords
used_fragments = {} # (middle_position, length) => count
# do the simulation: pick insert size from normal distribution, and
# position in genome from uniform distribution
x = 0
while x < read_pairs:
isize = int(random.normalvariate(options.mean_insert, options.insert_std))
while isize > len(ref) or isize < options.readlength:
isize = int(random.normalvariate(options.mean_insert, options.insert_std))
middle_pos = random.randint(ceil(0.5 *isize), floor(len(ref) - 0.5 * isize))
read_start1 = int(middle_pos - ceil(0.5 * isize))
read_start2 = read_start1 + isize - options.readlength
readname = ':'.join([ref.id, str(pair_counter), str(read_start1+1), str(read_start2+1)])
fragment = (middle_pos, isize)
if fragment in used_fragments:
used_fragments[fragment] += 1
readname += '.dup.' + str(used_fragments[fragment])
else:
used_fragments[fragment] = 1
read1 = sequences.Fastq(readname + '/1', ref.seq[read_start1:read_start1 + options.readlength], 'I' * options.readlength)
read2 = sequences.Fastq(readname + '/2', ref.seq[read_start2:read_start2 + options.readlength], 'I' * options.readlength)
if options.no_n and ('n' in read1.seq or 'N' in read1.seq or 'n' in read2.seq or 'N' in read2.seq):
continue
read2.revcomp()
print(read1, file=fout)
print(read2, file=fout)
if options.fragments:
frag = sequences.Fasta(readname, ref.seq[read_start1:read_start2 + options.readlength])
print(frag, file=fout_frags)
pair_counter += 1
x += 1
utils.close(fout)
if options.fragments:
utils.close(fout_frags)
def setUp(self):
self.fasta = sequences.Fasta('ID', 'ACGTA')
def test_make_into_gene_fasta(self):
'''Test make_into_gene fasta'''
print('sequences.genetic_code', sequences.genetic_code)
tests = [
(sequences.Fasta('ID', 'T'), None),
(sequences.Fasta('ID', 'TT'), None),
(sequences.Fasta('ID', 'TTT'), None),
(sequences.Fasta('ID', 'TTG'), None),
(sequences.Fasta('ID', 'TAA'), None),
(sequences.Fasta('ID', 'TTGAAATAA'), (sequences.Fasta('ID', 'TTGAAATAA'), '+', 0)),
(sequences.Fasta('ID', 'TTGAAATAT'), None),
(sequences.Fasta('ID', 'TTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)),
(sequences.Fasta('ID', 'TTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)),
(sequences.Fasta('ID', 'TTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 0)),
(sequences.Fasta('ID', 'TTGTAAAAA'), None),
(sequences.Fasta('ID', 'ATTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)),
(sequences.Fasta('ID', 'ATTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)),
(sequences.Fasta('ID', 'ATTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 1)),
(sequences.Fasta('ID', 'ATTGTAAAAA'), None),
(sequences.Fasta('ID', 'AATTGTAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)),
(sequences.Fasta('ID', 'AATTGTAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)),
(sequences.Fasta('ID', 'AATTGTAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '+', 2)),
(sequences.Fasta('ID', 'AATTGTAAAAA'), None),
(sequences.Fasta('ID', 'TTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)),
(sequences.Fasta('ID', 'ATTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)),
(sequences.Fasta('ID', 'AATTACAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 0)),
(sequences.Fasta('ID', 'AAATTACAA'), None),
(sequences.Fasta('ID', 'TTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)),
(sequences.Fasta('ID', 'ATTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)),
(sequences.Fasta('ID', 'AATTACAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 1)),
(sequences.Fasta('ID', 'AAATTACAAA'), None),
(sequences.Fasta('ID', 'TTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)),
(sequences.Fasta('ID', 'ATTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)),
(sequences.Fasta('ID', 'AATTACAAAA'), (sequences.Fasta('ID', 'TTGTAA'), '-', 2)),
(sequences.Fasta('ID', 'AAATTACAAAA'), None),
]
for seq, expected in tests:
self.assertEqual(seq.make_into_gene(), expected)
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_subseq(self):
'''Test subseq'''
fa = sequences.Fasta('name', 'ACGTA')
self.assertEqual(fa.subseq(1,4), sequences.Fasta('name', 'CGT'))
self.assertEqual(fa.subseq(None,4), sequences.Fasta('name', 'ACGT'))
self.assertEqual(fa.subseq(1,None), sequences.Fasta('name', 'CGTA'))
def test_is_all_Ns(self):
'''Test is_all_Ns()'''
self.assertTrue(sequences.Fasta('ID', 'n').is_all_Ns())
self.assertTrue(sequences.Fasta('ID', 'N').is_all_Ns())
self.assertTrue(sequences.Fasta('ID', 'nNn').is_all_Ns())
self.assertFalse(sequences.Fasta('ID', 'a').is_all_Ns())
self.assertFalse(sequences.Fasta('ID', '').is_all_Ns())
self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns())
self.assertFalse(sequences.Fasta('ID', 'naN').is_all_Ns())
self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=0, end=0))
self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=0, end=1))
self.assertTrue(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=1))
self.assertTrue(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=2))
self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(start=1))
self.assertTrue(sequences.Fasta('ID', 'anN').is_all_Ns(start=1))
self.assertFalse(sequences.Fasta('ID', 'anNg').is_all_Ns(end=1))
self.assertTrue(sequences.Fasta('ID', 'nNA').is_all_Ns(end=1))
with self.assertRaises(sequences.Error):
sequences.Fasta('ID', 'anNg').is_all_Ns(start=1, end=0)
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])
def test_replace_bases(self):
'''Check that bases get replaced correctly'''
fa = sequences.Fasta('X', 'AUCGTUUACT')
fa.replace_bases('U', 'T')
self.assertEqual(fa, sequences.Fasta('X', 'ATCGTTTACT'))