def __init__(self, args):
self.sample_file = args.infile
self.var_type = args.var_type
self.ref = args.ref
self.refidx = args.ref + '.fai'
self.min_af = args.min_AF
self.skip_on = args.skip_on
self.q = GridEngineQueue()
self.hold_jid = {}
self._regist_caller(args)
self._prepare_dir()
class Somatic:
def __init__(self, args):
self.sample_file = args.infile
self.var_type = args.var_type
self.ref = args.ref
self.refidx = args.ref + '.fai'
self.min_af = args.min_AF
self.skip_on = args.skip_on
self.q = GridEngineQueue()
self.hold_jid = {}
self._regist_caller(args)
self._prepare_dir()
@property
def worker_name(self):
return re.sub("(?!^)([A-Z]+)", r" \1", type(self).__name__).lower().split()[0]
@property
def sample_name(self):
clname = os.path.splitext(os.path.basename(self.clone))[0]
tiname = os.path.splitext(os.path.basename(self.tissue))[0]
return '{}_-_{}'.format(clname, tiname)
@property
def bin_path(self):
return os.path.dirname(os.path.realpath(__file__))
@property
def script_dir(self):
return '{}/job_scripts/{}'.format(self.bin_path, self.worker_name)
@property
def qerr_dir(self):
return 'q.err/{}.all'.format(self.sample_name)
@property
def qout_dir(self):
return 'q.out/{}.all'.format(self.sample_name)
@property
def af_dir(self):
return self.worker_name + '.AF'
@property
def out_dir(self):
return self.worker_name + '.out'
@property
def sample_list(self):
pairs = set()
with open(self.sample_file) as f:
for line in f:
try:
clone, tissue = line.split()[:2]
pairs.add((clone, tissue))
except ValueError as e:
msg = 'Sample list file should have at least 2 columns.'
raise e(msg)
return pairs
@property
def concall_file(self):
return '{}/{}.{}_call_n{}_{}AFcutoff.txt'.format(
self.out_dir, self.sample_name, self.var_type,
len(self.caller), str(self.min_af).replace('0.', ''))
@property
def concall_file_ok(self):
return self.skip_on and checksum_match(self.concall_file)
@staticmethod
def _check_ref(fasta):
if not os.path.isfile(fasta):
msg = "Can't find the reference file '{}'".format(fasta)
raise FileNotFoundError(msg)
if not os.path.isfile(fasta + '.fai'):
msg = "Can't find index for the fasta file '{}'".format(fasta)
raise FileNotFoundError(msg)
refname = os.path.splitext(fasta)[0]
if not os.path.isfile(refname + '.dict'):
msg = "Can't find dictionary for the fasta file '{}'".format(fasta)
raise FileNotFoundError(msg)
@staticmethod
def _check_bam(bam):
if not os.path.isfile(bam):
msg = "Can't find the bam file '{}'".format(bam)
raise FileNotFoundError(msg)
bamname = os.path.splitext(bam)[0]
if not os.path.isfile(bamname + '.bai') and not os.path.isfile(bamname + '.bam.bai'):
msg = "Can't find index for the bam file '{}'".format(bam)
raise FileNotFoundError(msg)
def _regist_caller(self, args):
if self.var_type == "snv":
self.caller = [SomaticSniper(args, self.worker_name),
Strelka(args, self.worker_name)]
if args.chunk_on:
chunk_size = 25000000
chunk_file = self._chunkfile(chunk_size)
self.caller.extend([
MuTect(args, self.worker_name, chunk_file),
VarScan(args, self.worker_name, chunk_file)])
else:
self.caller.extend([
MuTect(args, self.worker_name),
VarScan(args, self.worker_name)])
elif self.var_type == "indel":
self.caller = [Strelka(args, self.worker_name)]
if args.chunk_on:
chunk_size = 25000000
chunk_file = self._chunkfile(chunk_size)
chrom_file = self._chromfile()
self.caller.extend([
Scalpel(args, self.worker_name, chrom_file),
VarScan(args, self.worker_name, chunk_file)])
else:
self.caller.extend([
Scalpel(args, self.worker_name),
VarScan(args, self.worker_name)])
def _prepare_dir(self):
make_dir(self.out_dir)
def _check_data(self):
self._check_ref(self.ref)
for clone, tissue in self.sample_list:
self._check_bam(clone)
self._check_bam(tissue)
def _qopt(self, jprefix, hold_jid=''):
qopt = '-N {}.{} -e {} -o {} -v BIN_PATH={}'.format(
jprefix, self.sample_name, self.qerr_dir, self.qout_dir, self.bin_path)
if hold_jid == '':
return qopt
else:
return qopt + ' -hold_jid {}'.format(hold_jid)
def _chunkfile(self, chunk_size):
f=lambda n,i=0:"{:.0f}{}".format(n," kMG"[i])*(n<1e3)or f(n/1e3, i+1)
chunk_file = "{}.call/genomic_regions_{}_chunk.txt".format(
self.worker_name, f(chunk_size).strip())
if not os.path.isfile(chunk_file):
make_dir(os.path.dirname(chunk_file))
with open(chunk_file, 'w') as out:
with open(self.refidx) as f:
for line in f:
chrom, chrom_size = line.split()[:2]
chrom_size = int(chrom_size)
for start in range(1, chrom_size, chunk_size):
end = start + chunk_size - 1
if end > chrom_size:
end = chrom_size
out.write('{}:{}-{}\n'.format(chrom, start, end))
return chunk_file
def _chromfile(self):
chrom_file = "{}.call/genomic_regions_chrom.txt".format(
self.worker_name)
if not os.path.isfile(chrom_file):
make_dir(os.path.dirname(chrom_file))
with open(chrom_file, 'w') as out:
with open(self.refidx) as f:
chroms = []
for line in f:
chrom, chrom_size = line.split()[:2]
chrom_size = int(chrom_size)
chroms.append((chrom, chrom_size))
chroms.sort(key=lambda chrom:chrom[1], reverse=True)
for chrom, end in chroms:
out.write('{}:1-{}\n'.format(chrom, end))
return chrom_file
def _concall(self, hold_jid):
qopt = self._qopt('con_call', hold_jid)
cmd = '{}/{}_con_call.sh {} {} {}'.format(
self.script_dir, self.var_type,
self.min_af, self.af_dir, self.concall_file)
return self.q.submit(qopt, cmd)
def _skip_msg(self, jname):
if self.q.__class__.is_1st_print:
self.q.__class__.is_1st_print = False
else:
print('\x1b[2A', end='\r')
skip_msg(jname, '{}.all'.format(self.sample_name))
def _run_msg(self, jname):
run_msg(jname, '{}.all'.format(self.sample_name))
def _run(self):
hold_jid = ''
if self.concall_file_ok:
self._skip_msg('calling')
self._skip_msg('af_calc')
self._skip_msg('con_call')
else:
make_dir(self.qerr_dir)
make_dir(self.qout_dir)
jids = (caller.run(self.clone, self.tissue) for caller in self.caller)
hold_jid = ','.join(jid for jid in jids if jid != '')
hold_jid = self._concall(hold_jid)
self._run_msg('con_call')
return hold_jid
def run(self):
self._check_data()
for clone, tissue in self.sample_list:
self.clone = clone
self.tissue = tissue
self._run()
end_msg(self.q.j_total)