def test_3_generate_mixed_dataset(self):
""" Generates a mixed synthetic dataset of eschColi with reads[0] reads
and dm3 with reads[1] reads.
"""
orgs = [os.path.join(self.reference, "eschColi_K12/seq/eschColi_K12.fa"),
os.path.join(self.reference, "dm3/seq/dm3.fa")]
reads = [3000, 6000]
# Will hold the real number of fastq reads after simNGS, independent of
# organism
lines = []
dst = os.path.join(self.synthetic_fastq,
"simngs.mixed_{org1}_{org2}_{reads1}vs{reads2}.fastq".format(org1='eschColi_K12',
org2='dm3',
reads1=reads[0],
reads2=reads[1]))
for org, read in izip(orgs, reads):
fa_entries = 0
with open(org, 'r') as cnt:
for line in cnt:
if '>' in line:
fa_entries += 1
with open(dst, 'a') as fh:
n = str(ceil(read/float(fa_entries)))
cl1 = [self.simlib, "--seed", self.sim_seed, "-n", n, org]
cl2 = [self.simngs, "-s", self.sim_seed, "-o", "fastq", self.runfile]
p1 = subprocess.Popen(cl1, stdout=subprocess.PIPE)
p2 = subprocess.Popen(cl2, stdin=p1.stdout, stdout=fh).communicate()
p1.stdout.close()
#trim_fastq will trim the excess of dm3 reads, as they're the last ones,
#leading to a file with exactly 3000 reads of E.choli and 6000 of dm3
helpers.trim_fastq(dst, sum(reads))
def test_2_run_simNGS(self):
""" Simulates an Illumina run with simNGS read simulator
for each organism in references directory.
"""
# Generate N simulated reads of every organism present in "org"
orgs = [o for o in glob.glob(os.path.join(self.reference, "*/seq/*.fa"))]
for org in orgs:
for reads in self.sim_reads:
dst = os.path.join(self.synthetic_fastq,
"simngs_{org}_{reads}.fastq".format(org=org.split(os.sep)[-3], reads=reads))
#Do not regenerate datasets that are already present
if not os.path.exists(dst):
fa_entries = 0
# Determine how many FASTA "Description lines" (headers) there are
# since simNGS will generate reads depending on that number
with open(org, 'r') as cnt:
for line in cnt:
if '>' in line:
fa_entries += 1
with open(dst, 'w') as fh:
n = str(ceil(reads/float(fa_entries)))
cl1 = [self.simlib, "--seed", self.sim_seed, "-n", n, org]
cl2 = [self.simngs, "-s", self.sim_seed, "-o", "fastq", self.runfile]
# XXX: To be parametrized in future benchmarks (for paired end reads)
#cl2 = [simngs, "-o", "fastq", "-p", "paired", runfile]
# http://docs.python.org/2/library/subprocess.html#replacing-shell-pipeline
p1 = subprocess.Popen(cl1, stdout=subprocess.PIPE)
p2 = subprocess.Popen(cl2, stdin=p1.stdout, stdout=fh).communicate()
p1.stdout.close()
#Trim the FAST file to the actual number of reads
helpers.trim_fastq(dst, reads)
