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worker.py
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worker.py
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import os
from itertools import permutations
from job_queue import GridEngineQueue
from utils import (
make_dir,
checksum_match,
skip_msg,
run_msg,
end_msg)
from caller import (
MuTect,
SomaticSniper,
Scalpel,
Strelka,
VarScan)
class Somatic:
def __init__(self, args):
self.sample_file = args.infile
self.var_type = args.var_type
self.min_af = args.min_AF
self.skip_on = args.skip_on
self.chunk_size = args.chunk_size
self.q = GridEngineQueue()
self.hold_jid = {}
self._regist_caller(args)
self._prepare_dir()
@property
def worker_name(self):
return type(self).__name__.lower()
@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:
clone, tissue = line.strip().split('\t')[:2]
pairs.add((clone, tissue))
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)
@property
def chunk_file(self):
f=lambda n,i=0:"{:.0f}{}".format(n," kMG"[i])*(n<1e3)or f(n/1e3, i+1)
return "{}.call/genomic_regions_{}_chunk.txt".format(
self.worker_name, f(self.chunk_size).strip())
@property
def chrom_file(self):
return "{}.call/genomic_regions_chrom.txt".format(self.worker_name)
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:
self.caller.extend([
MuTect(args, self.worker_name, self.chunk_file),
VarScan(args, self.worker_name, self.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:
self.caller.extend([
Scalpel(args, self.worker_name, self.chrom_file),
VarScan(args, self.worker_name, self.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 _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 _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):
for clone, tissue in self.sample_list:
self.clone = clone
self.tissue = tissue
self._run()
end_msg(self.q.j_total)
class Sensitivity(Somatic):
def __init__(self, args):
super().__init__(args)
self.control_bam = args.control_bam
self.control_var = args.control_var
self.g1k_var = args.g1k_var
self.germ_het_var = args.germ_het_var
if self.true_file_ok:
self.true_jid = ''
self.q.__class__.is_1st_print = False
skip_msg('truefile', 'For all samples')
else:
self.true_jid = self._truefile()
run_msg('truefile', 'For all samples')
@property
def sample_list(self):
pairs = set()
with open(self.sample_file) as f:
for line in f:
clone = line.strip().split('\t')[0]
pairs.add((clone, self.control_bam))
return pairs
@property
def concall_file(self):
return '{}/{}.call_n{{}}.{}_AF.txt'.format(
self.af_dir, self.sample_name, self.var_type)
@property
def concall_file_ok(self):
return self.skip_on and all(
[checksum_match(self.concall_file.format(i))
for i in range(1,len(self.caller)+1)])
@property
def true_file(self):
if self.var_type == "snv":
var_type = "snp"
else:
var_type = self.var_type
return '{}/germ_het_not_in_NA12878_{}.txt'.format(
self.out_dir, var_type)
@property
def true_file_ok(self):
return self.skip_on and checksum_match(self.true_file)
@property
def sens_file(self):
return "{}/{}.{}_sensitivity_{}AFcutoff.txt".format(
self.out_dir, self.sample_name, self.var_type,
str(self.min_af).replace('0.', ''))
@property
def sens_file_ok(self):
return self.skip_on and checksum_match(self.sens_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.sample_name)
return self.q.submit(qopt, cmd)
def _truefile(self):
qopt = '-N true_file -e q.err -o q.out'
cmd = '{}/true_file.sh {} {} {} {}'.format(
self.script_dir, self.control_var, self.g1k_var,
self.germ_het_var, self.true_file)
return self.q.submit(qopt, cmd)
def _sensitivity(self, hold_jid):
qopt = self._qopt('sens', hold_jid)
cmd = '{}/{}_sensitivity.sh {} {} {} {}'.format(
self.script_dir, self.var_type,
self.min_af, self.true_file, self.af_dir, self.sens_file)
return self.q.submit(qopt, cmd)
def _run(self):
if self.sens_file_ok:
self._skip_msg('calling')
self._skip_msg('af_calc')
self._skip_msg('con_call')
self._skip_msg('sens')
else:
make_dir(self.qerr_dir)
make_dir(self.qout_dir)
hold_jid = super()._run()
if hold_jid == '':
hold_jid = self.true_jid
elif self.true_jid != '':
hold_jid += ',' + self.true_jid
self._sensitivity(hold_jid)
self._run_msg('sens')
class Pairwise(Somatic):
def __init__(self, args):
super().__init__(args)
self.out_prefix = args.out_prefix
if self.out_prefix != '':
self.out_prefix += '-'
@property
def sample_list(self):
clones = set()
with open(self.sample_file) as f:
for line in f:
clones.add(line.strip().split('\t')[0])
return permutations(clones, 2)
@property
def concall_dir(self):
return '{}/concall'.format(self.out_dir)
@property
def concall_file(self):
return '{}/{}.{}_call_n{}_{}AFcutoff.txt'.format(
self.concall_dir, self.sample_name, self.var_type,
len(self.caller), str(self.min_af).replace('0.', ''))
@property
def explscore_file(self):
return '{}/{}pairwise_union.{}_call_n{}_{}AFcutoff.expl_score.txt'.format(
self.out_dir, self.out_prefix, self.var_type,
len(self.caller), str(self.min_af).replace('0.',''))
@property
def explscore_file_ok(self):
return self.skip_on and checksum_match(self.explscore_file)
def _prepare_dir(self):
make_dir(self.concall_dir)
def _explscore(self, hold_jid):
concall_flist = '{}/{}concall_list.{}_call_n{}_{}AFcutoff.txt'.format(
self.out_dir, self.out_prefix, self.var_type,
len(self.caller), str(self.min_af).replace('0.',''))
with open(concall_flist, 'w') as out:
for clone, tissue in self.sample_list:
self.clone = clone
self.tissue = tissue
out.write(self.concall_file + '\n')
qopt = '-N expl_score -e q.err -o q.out -v BIN_PATH={}'.format(self.bin_path)
if hold_jid != '':
qopt += ' -hold_jid {}'.format(hold_jid)
cmd = '{}/expl_score.sh {} {}'.format(
self.script_dir, concall_flist, self.explscore_file)
return self.q.submit(qopt, cmd)
def run(self):
if self.explscore_file_ok:
self._skip_msg('calling')
self._skip_msg('af_calc')
self._skip_msg('con_call')
self._skip_msg('expl_score')
else:
jids = []
for clone, tissue in self.sample_list:
self.clone = clone
self.tissue = tissue
jids.append(super()._run())
hold_jid = ','.join(jid for jid in jids if jid != '')
self._explscore(hold_jid)
self._run_msg('expl_score')
end_msg(self.q.j_total)