def assemble_paired_end_reads(args, velvet_optimiser, indiv, read, interleaved_dir):
assert is_dir(interleaved_dir), IOError("Directory {} containing interleaved reads does not exist".format(interleaved_dir))
singletons = os.path.join(
interleaved_dir,
"{0}{1}".format(indiv, '-READ-singleton.fastq.gz')
)
interleaved = os.path.join(
interleaved_dir,
"{0}{1}".format(indiv, '-READ1and2-interleaved.fastq.gz')
)
for f in [singletons, interleaved]:
assert os.path.isfile(f), IOError("Missing sequence file(s): {0}".format(f))
assembly_dir = os.path.join(args.output, indiv, 'assembly')
mkdir_p(assembly_dir)
os.chdir(assembly_dir)
velveth = "-fastq.gz -shortPaired {} -short {}".format(singletons, interleaved)
cmd = [velvet_optimiser,
"-s", args.s,
"-e", args.e,
"-c", "'ncon'",
"-t", args.t,
"-a",
"-f", velveth
]
stdout, stderr = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE).communicate()
return stdout, stderr, assembly_dir