def setUpClass(cls):
fastqs = os.path.join(os.path.dirname(__file__), 'fastqs')
cls.fname = os.path.join(fastqs, 'test_engine.fastq')
cls.fname_1 = os.path.join(fastqs, 'test_engine_1.fastq')
cls.fname_2 = os.path.join(fastqs, 'test_engine_2.fastq')
engine.config(nthreads=1)
cls.tfn = tempfile.NamedTemporaryFile(suffix='.fastq', delete=False)
def test_forward_fastq(self):
engine.config(Amin='#', nthreads=2, minoverlap=80)
for n in [3, 5, 7, 133]:
for plus in ['+', '+IDENTIFIER']:
for cr in ['\n', '\r\n']:
record = '@IDENTIFIER' + cr + 'A' * 80 + cr + \
plus + cr + '#' * 80 + cr
file(self.tfn.name, 'wb').write(record * n)
Fastq(self.tfn.name, quiet=True)
ret = engine.findseqs(self.tfn.name, ['A'*80])
assert len(ret['hits']) == n
def test_Amin(self):
seqs = (
"GGAG",
"CCGAC",
)
engine.config(Amin='H', minreadlength=4, maxerrors=0)
ret = engine.findseqs(self.fname, seqs)
assert len(ret['hits']) == 1
assert ret['stats']['readlengths'][5] == 3
assert ret['stats']['readlengths'][4] == 5
engine.config(Amin='G')
ret = engine.findseqs(self.fname, seqs)
assert len(ret['hits']) == 2
def test_hits(self):
fq = FastqGenerator(self.tfn.name, force=True)
seq = fq.randseq(51)
minoverlap = 25
readlength = 100
pmax = .05
n = 100
for i in range(n):
fq.cover_seq(seq,
minoverlap=minoverlap,
readlength=readlength,
pmax=pmax)
fq.flush()
#print "\033[94mfilesize=%.2f MB\033[m" % (fq.size() / 1024. / 1024.)
fq = Fastq(self.tfn.name, quiet=True)
engine.config(
nthreads=3,
Amin=fq.Q2A(fq.p2Q(pmax)),
maxerrors=0,
minreadlength=random.randint(minoverlap, readlength),
minoverlap=minoverlap
)
ret = engine.findseqs(fq.fname, [seq])
assert ret['stats']['readlengths'][readlength] == n
assert len(ret['hits']) == n
if 0:
print('hits=%d'%len(ret['hits']))
print('readlenghts='+', '.join(['%dx %dbp'%(n, idx)
for idx,n in enumerate(ret['stats']['readlengths']) if n]))
seqx = ''.join([i%minoverlap!=0 and b or {'A':'C','C':'G','G':'T','T':'A'}[b]
for i,b in enumerate(seq)])
ret = engine.findseqs(fq.fname, [seqx])
if 0:
print('0123456789'*6)
print(('*'+' '*(minoverlap-1))*6)
print(seq)
print(seqx)
print(str(ret['hits']))
assert ret['stats']['readlengths'][readlength] == n
assert len(ret['hits']) == 0
def test_maxerror(self):
''' test different values for ``maxerror`` config parameter '''
engine.config(minreadlength=25, minoverlap=25, Amin='!')
seqs = (
#GAGCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT
"CAGCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT",
#^ : 1 error
"CTGCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT",
#^^: 2 errors
"CTCCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT",
#^^^: 3 errors
)
for maxerrors in range(4):
engine.config( maxerrors=maxerrors )
hits = engine.findseqs(self.fname, seqs)['hits']
assert len(hits) == maxerrors
def test_minoverlap(self):
''' test different values for ``minoverlap`` config parameter '''
seqs = (
"TCGATGCGATCTGTCAAGTCGGTGGCGGTA...", # end of sequence + junk
"TCGATGCGATCTG.CAAGTCGGTGGCGGTA...", # end of sequence + junk + 1 error
"...NTGAACGTATCGCCTCGAGGGACTT", # junk + beginning of sequence
"...NTGAACGTATCG.CTCGAGGGACTT", # junk + beginning of sequence + 1 error
)
engine.config(
maxerrors=0,
minreadlength=25,
minoverlap=30,
Amin='!'
)
ret = engine.findseqs(self.fname, seqs)
hits = ret['hits']
assert len(hits)==1 and hits[0].seq_nr==0 and hits[0].seq_pos<0
engine.config(maxerrors=0, minoverlap=25)
hits = engine.findseqs(self.fname, seqs)['hits']
assert len(hits)==2
for hit in hits:
assert hit[0]!=3 or hit[2]>0
engine.config(maxerrors=1, minoverlap=25)
hits = engine.findseqs(self.fname, seqs)['hits']
assert len(hits)==4
def test_paired(self, gz=False):
engine.config(maxerrors=0, minoverlap=1000, minreadlength=3, Amin='!')
seqs = (
"CCC", # "CCCC" should be counted 2x ...
"TTTT",
"TATATATA",
"TGTAG", # at beginning
"ATATT", # at end
"GAGCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT",
"...NACTTCCTCTCTACTGGTGTCGGCGGTGAAAGAGCTTACGTACTCTTCGAT...",
)
fname = self.fname
fnames = (self.fname_1, self.fname_2)
if gz:
fname += '.gz'
fnames = (self.fname_1 + '.gz', self.fname_2 + '.gz')
ret = engine.findseqs(fname, seqs)
ret_12 = engine.findseqs(fnames, seqs)
assert ret == ret_12
def test_findseqs(self, gz=False):
''' find specified sequences in handwritten .fastq file '''
engine.config(maxerrors=0, minoverlap=1000, minreadlength=3, Amin='!')
seqs = (
"CCC", # "CCCC" should be counted 2x ...
"TTTT",
"TATATATA",
"TGTAG", # at beginning
"ATATT", # at end
"GAGCATGTGGAGCAACTTGTGGGAGCGCCGGGCAACGCCCTGTCTCTTAT",
"...NACTTCCTCTCTACTGGTGTCGGCGGTGAAAGAGCTTACGTACTCTTCGAT...",
)
fname = self.fname
if gz:
fname += '.gz'
hits = engine.findseqs(fname, seqs)['hits']
if gz:
f = gzip.GzipFile(fname, 'rb')
else:
f = file(fname, 'rb')
x = [0] * len(seqs)
for hit in hits:
x[hit.seq_nr] += 1
seq = seqs[hit.seq_nr]
if hit.seq_pos<0:
f.seek(hit.file_pos-hit.seq_pos)
bps = f.read(hit.length)
else:
f.seek(hit.file_pos)
bps = f.read(hit.length)
seq = seq[hit.seq_pos:hit.seq_pos+hit[3]]
assert bps == seq
assert x == [19,1,0,1,1,1,1]
def setUp(self):
engine.config(nthreads=1, maxerrors=2, minoverlap=25,
Amin='!', Azero='!')
sys.stderr.write('\n*** you must specify at least one testsuite! ***\n\n')
sys.stderr.write('(use the -t command line switch)\n\n')
sys.exit(ERROR_COMMAND_LINE_SWITCH)
# prepare scanning {{{2
try:
fastq = Fastq(args.fastq, paired=not args.no_paired, variant=args.variant)
except FastqFileFormatException, e:
lo.error('cannot open file %s : %s'%(args.fastq, str(e)))
sys.exit(ERROR_FASTQ_FORMAT_ERROR)
engine.config(
nthreads=args.threads,
maxerrors=args.errors,
Amin=fastq.Q2A(args.quality),
Azero=fastq.Azero,
minreadlength=args.readlength,
minoverlap=args.overlap
)
analyser = analyse.Analyser()
if not args.force:
if os.path.exists(args.json):
lo.error('will not overwrite file ' + args.json)
sys.exit(ERROR_FILE_EXISTS)
if args.extract_hits and os.path.exists(args.extract_hits):
lo.error('will not overwrite file ' + args.extract_hits)
sys.exit(ERROR_FILE_EXISTS)
# do scanning {{{2
