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 = [
'fastn_unittest_fail_no_AT.fq', 'fastn_unittest_fail_no_seq.fq',
'fastn_unittest_fail_no_plus.fq', 'fastn_unittest_fail_no_qual.fq'
]
for fname in bad_files:
f_in = utils.open_file_read(fname)
fq = fastn.Fastq()
with self.assertRaises(fastn.Error):
while fq.get_next_from_file(f_in):
pass
utils.close(f_in)
fname = 'fastn_unittest_good_file.fq'
try:
f_in = open(fname)
except IOError:
print("Error opening '" + fname + "'", file=sys.stderr)
sys.exit(1)
fq = fastn.Fastq()
while fq.get_next_from_file(f_in):
self.assertEqual(fq, fastn.Fastq('ID', 'ACGTA', 'IIIII'))
utils.close(f_in)
def test_to_fastn(self):
'''Check conversion to fastq with to_fastq()'''
sams = [
sam.SamRecord(
'ID\t0\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\tIIIII'),
sam.SamRecord(
'ID\t16\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\tIIIII'),
sam.SamRecord(
'ID\t65\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\tIIIII'),
sam.SamRecord(
'ID\t129\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\tIIIII'),
sam.SamRecord('ID\t0\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\t*'),
sam.SamRecord('ID\t16\tref\t1\t47\t2S73M\t=\t362\t438\tACGTA\t*')
]
seqs = [
fastn.Fastq('ID', 'ACGTA', 'IIIII'),
fastn.Fastq('ID', 'TACGT', 'IIIII'),
fastn.Fastq('ID/1', 'ACGTA', 'IIIII'),
fastn.Fastq('ID/2', 'ACGTA', 'IIIII'),
fastn.Fasta('ID', 'ACGTA'),
fastn.Fasta('ID', 'TACGT')
]
for i in range(len(sams)):
self.assertEqual(seqs[i], sams[i].to_fastn())
def test_translate(self):
'''Test nucleatide -> amino acid conversion works on Fasta'''
fq = fastn.Fastq(
'ID',
'GCAGCCGCGGCTAGAAGGCGACGCCGGCGTAACAATGACGATTGCTGTGAAGAGCAACAGGGAGGCGGGGGTCACCATATAATCATTTTATTGCTACTCCTGCTTAAAAAGATGTTCTTTCCACCCCCGCCTAGCAGTTCATCCTCGTCTACAACCACGACTTGGTACTATGTAGTCGTGGTTTAATAGTGA',
'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'
)
self.assertEqual(
fastn.Fastq(
'ID',
'AAAARRRRRRNNDDCCEEQQGGGGHHIIILLLLLLKKMFFPPPPSSSSSSTTTTWYYVVVV***',
'IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII'
), fq.translate())
def test_trim(self):
'''trim() should trim the right number of bases off start and end'''
fq = fastn.Fastq('ID', '1234567890', '1234567890')
fq.trim(0, 0)
self.assertEqual(fq, fastn.Fastq('ID', '1234567890', '1234567890'))
fq = fastn.Fastq('ID', '1234567890', '1234567890')
fq.trim(1, 0)
self.assertEqual(fq, fastn.Fastq('ID', '234567890', '234567890'))
fq = fastn.Fastq('ID', '1234567890', '1234567890')
fq.trim(0, 1)
self.assertEqual(fq, fastn.Fastq('ID', '123456789', '123456789'))
fq = fastn.Fastq('ID', '1234567890', '1234567890')
fq.trim(2, 2)
self.assertEqual(fq, fastn.Fastq('ID', '345678', '345678'))
def to_fastn(self):
if self.qual == '*':
seq = fastn.Fasta(self.id, self.seq)
else:
seq = fastn.Fastq(self.id, self.seq, self.qual)
if self.query_strand() == '-':
seq.revcomp()
if self.is_first_of_pair():
seq.id += '/1'
elif self.is_second_of_pair():
seq.id += '/2'
return seq
def test_trim_Ns(self):
'''trim_Ns() should do the right trimming of a fastq sequence'''
fq = fastn.Fastq('ID', 'ANNANA', '111111')
test_seqs = [
fastn.Fastq('ID', 'ANNANA', '111111'),
fastn.Fastq('ID', 'NANNANA', '1111111'),
fastn.Fastq('ID', 'NANNANAN', '11111111'),
fastn.Fastq('ID', 'ANNANAN', '1111111'),
fastn.Fastq('ID', 'NNNNNNANNANAN', '1111111111111'),
fastn.Fastq('ID', 'NNANNANANn', '1111111111')
]
for s in test_seqs:
s.trim_Ns()
self.assertEqual(fq, s)
def test_file_reader_fastq(self):
'''file_reader should iterate through a fastq file correctly'''
reader = fastn.file_reader('fastn_unittest_good_file.fq')
for seq in reader:
self.assertEqual(seq, fastn.Fastq('ID', 'ACGTA', 'IIIII'))
def test_to_Fasta_and_qual(self):
'''Check to_Fasta_and_qual converts quality scores correctly'''
fq = fastn.Fastq('ID', 'ACGT', '>ADI')
(fa, qual) = fq.to_Fasta_and_qual()
self.assertEqual(fa, fastn.Fasta('ID', 'ACGT'))
self.assertListEqual(qual, [29, 32, 35, 40])
def test_revcomp(self):
'''revcomp() should correctly reverse complement a sequence'''
fq = fastn.Fastq('ID', 'ACGTNacgtn', '1234567890')
fq.revcomp()
self.assertEqual(fq, fastn.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(fastn.Error):
fastn.Fastq('X', 'A', 'II')
def setUp(self):
self.fastq = fastn.Fastq('ID', 'ACGTA', 'IIIII')
def test_to_Fastq(self):
'''Check to_Fastq converts OK, including out of range quality scores'''
fa = fastn.Fasta('X', 'AAAAA')
quals = [-1, 0, 40, 93, 94]
self.assertEqual(fastn.Fastq('X', 'AAAAA', '!!I~~'),
fa.to_Fastq(quals))
options = parser.parse_args()
ref_seqs = {}
fastn.file_to_dict(options.ref_in, ref_seqs)
sam_reader = sam.file_reader(options.bam_in)
reads = {}
f1 = utils.open_file_write(options.outprefix + '_1.fq')
f2 = utils.open_file_write(options.outprefix + '_2.fq')
for s in sam_reader:
if s.is_mapped() and s.is_mate_mapped():
end = min(s.pos + options.length - 1, len(ref_seqs[s.rname]) - 1)
start = max(end - options.length + 1, 0)
read = fastn.Fastq(s.id, ref_seqs[s.rname][start:end + 1],
'I' * (end - start + 1))
if not s.is_forward_strand():
read.revcomp()
if read.id in reads:
if s.is_first_of_pair():
read.id += '/1'
mate = reads[s.id]
mate.id += '/2'
print(read, file=f1)
print(mate, file=f2)
else:
read.id += '/2'
mate = reads[s.id]
mate.id += '/1'
if len(seq) < options.read_length:
end_range = 1
for i in range(0, end_range, options.read_step):
if len(seq) <= options.read_length:
start = 0
end = len(seq) - 1
else:
start = i
end = start + options.read_length - 1
if end > len(seq) - 1:
end = len(seq) - 1
start = end - options.read_length + 1
read = fastn.Fastq(
options.read_prefix + ':' + seq.id + ':' + str(start + 1) + ':' +
str(end + 1), seq[start:end + 1], 'I' * (end - start + 1))
print('\t'.join([
read.id, '0', seq.id,
str(start + 1), '60',
str(len(read)) + 'M', '*', '*', '*', read.seq, read.qual,
'RG:Z:' + options.read_group
]),
file=f)
if end == len(seq) - 1:
break
f.close()
while isize > len(ref) and 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 = fastn.Fastq(readname + '/1', ref.seq[read_start1:read_start1 + options.readlength], 'I' * options.readlength)
read2 = fastn.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)
pair_counter += 1
x += 1
utils.close(fout)