def analyse_wgs_prepare(self, input, output):
'''
creates working directory and scripts to run for wgs pipeline
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
if normal_id is None: # nothing to do
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
tmp_id = 'wgs-{}'.format(tumour_id)
tmp_dir = '{tmp}/{tmp_id}'.format(tmp=config.TMP, tmp_id=tmp_id)
safe_make_dir(tmp_dir)
safe_make_dir(os.path.dirname(output))
command = 'cp {root}/src/util/analysisWGS.serial.sh {tmp_dir}/analysisWGS.sh && cp {root}/src/util/ds-wrapper-wgs-1.0.8.pl {tmp_dir}/ds-wrapper.pl && touch {output}'.format(
root=config.ROOT, output=output, tmp_dir=tmp_dir)
run_stage(self.state, 'analyse_wgs_prepare', command)
def contest(self, input, output):
'''
run contest
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{root}/cfg/sample-metadata.csv".format(root=config.ROOT),
'r'))
# tumour_id is actually normal
if normal_id is None:
normal_id = tumour_id
validation_data = open(
"{root}/out/{sample}.validation".format(root=config.ROOT,
sample=normal_id),
'r').readlines()
normal_uuid = validation_data[1].split('\t')[8]
with open(
'{tmp_dir}/{tumour_id}.contest.sh'.format(
tmp_dir=config.TMP, tumour_id=tumour_id),
'w') as analyse_fh:
for line in open(
'{root}/src/util/contest.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('UUID', normal_uuid, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
analyse_fh.write(new_line)
else:
# it's a tumour
validation_data = open(
"{root}/out/{sample}.validation".format(root=config.ROOT,
sample=normal_id),
'r').readlines()
normal_uuid = validation_data[1].split('\t')[8]
with open(
'{tmp_dir}/{tumour_id}.contest.sh'.format(
tmp_dir=config.TMP, tumour_id=tumour_id),
'w') as analyse_fh:
for line in open(
'{root}/src/util/contest.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('UUID', normal_uuid, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
analyse_fh.write(new_line)
command = 'bash {tmp_dir}/{tumour_id}.contest.sh 2>{prefix}.contest.log.err 1>{prefix}.contest.log.out && touch "{output}"'.format(
tmp_dir=config.TMP,
tumour_id=tumour_id,
output=output,
prefix=prefix)
run_stage(self.state, 'contest', command)
def _analyse_wgs_with_command(self, input, output, subcommand, cpu=4):
'''
take mapped bams and generate variant calls by running the sanger pipeline cgpwgs
'''
input = input[0]
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
if normal_id is None: # nothing to do
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
tmp_id = 'wgs-{}-{}'.format(config.WGS_VERSION, tumour_id)
tmp_dir = '{tmp}/{tmp_id}'.format(tmp=config.TMP, tmp_id=tmp_id)
safe_make_dir('{}/home'.format(tmp_dir))
# make subcommand analysis script
with open(
'{tmp_dir}/analyse-{subcommand}.sh'.format(
tmp_dir=tmp_dir, subcommand=subcommand),
'w') as analyse_fh:
for line in open(
'{root}/src/util/analyse-{wgs_version}.sh.template'.format(
wgs_version=config.WGS_VERSION, root=config.ROOT),
'r'): #analyse-1.1.2.sh.template
new_line = re.sub('TMP_ID', tmp_id, line)
new_line = re.sub('TUMOUR', tumour_id, new_line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('COMMAND', subcommand, new_line)
new_line = re.sub('WGS_VERSION', config.WGS_VERSION, new_line)
new_line = re.sub('CPULIMIT', str(cpu), new_line)
analyse_fh.write(new_line)
command = 'singularity exec -i --bind {in_dir}:/mnt/in,{out}:/mnt/out,{reference}:/mnt/reference,{tmp}:/mnt/tmp --workdir {tmp_dir} --home {tmp_dir}/home:/home/z --contain {root}/img/cgpwgs-{wgs_version}.img bash /mnt/tmp/{tmp_id}/analyse-{subcommand}.sh 1>{prefix}.wgs.{subcommand}.{wgs_version}.log.out 2>{prefix}.wgs.{subcommand}.{wgs_version}.log.err && touch {output}'.format(
root=config.ROOT,
in_dir=config.IN,
out=config.OUT,
reference=config.REFERENCE,
tmp=config.TMP,
tmp_dir=tmp_dir,
tmp_id=tmp_id,
prefix=prefix,
output=output,
subcommand=subcommand,
wgs_version=config.WGS_VERSION)
run_stage(self.state, 'analyse_wgs_{}'.format(subcommand), command)
def callable_bases(self, input, output):
'''
run callable bases
'''
MINIMUM_COVERAGE_TUMOR = '17'
MINIMUM_COVERAGE_NORMAL = '10'
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{root}/cfg/sample-metadata.csv".format(root=config.ROOT),
'r'))
# nothing to do for normal sample
if normal_id is None:
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
# it's a tumour
with open(
'{tmp_dir}/{tumour_id}.callable_bases.sh'.format(
tmp_dir=config.TMP, tumour_id=tumour_id),
'w') as analyse_fh:
for line in open(
'{root}/src/util/callable_bases.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
new_line = re.sub('TMP_DIR', config.TMP, new_line)
new_line = re.sub('MIN_TUM', MINIMUM_COVERAGE_TUMOR, new_line)
new_line = re.sub('MIN_NORM', MINIMUM_COVERAGE_NORMAL,
new_line)
analyse_fh.write(new_line)
command = 'bash {tmp_dir}/{tumour_id}.callable_bases.sh 2>{prefix}.callable_bases.log.err 1>{prefix}.callable_bases.log.out && touch "{output}"'.format(
tmp_dir=config.TMP,
tumour_id=tumour_id,
output=output,
prefix=prefix)
run_stage(self.state, 'callable_bases', command)
def hmmcopy(self, input, output):
'''
run hmmcopy
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
# tumour_id is actually a normal
if normal_id is None:
target_dir = '{}.hmmcopy'.format(prefix)
safe_make_dir(target_dir)
with open('{target_dir}/hmmcopy.sh'.format(target_dir=target_dir),
'w') as analyse_fh:
for line in open(
'{root}/src/util/hmmcopy-normal.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('NORMAL', tumour_id, line)
new_line = re.sub('ROOT', config.ROOT, new_line)
new_line = re.sub('TARGET_DIR', target_dir, new_line)
analyse_fh.write(new_line)
command = 'bash {target_dir}/hmmcopy.sh 2>{prefix}.hmmcopy.log.err 1>{prefix}.hmmcopy.log.out && touch "{output}"'.format(
target_dir=target_dir, output=output, prefix=prefix)
else:
# it's a tumour
target_dir = '{}.hmmcopy'.format(prefix)
safe_make_dir(target_dir)
with open('{target_dir}/hmmcopy.sh'.format(target_dir=target_dir),
'w') as analyse_fh:
for line in open(
'{root}/src/util/hmmcopy.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
new_line = re.sub('TARGET_DIR', target_dir, new_line)
analyse_fh.write(new_line)
command = 'bash {target_dir}/hmmcopy.sh 2>{prefix}.hmmcopy.log.err 1>{prefix}.hmmcopy.log.out && touch "{output}"'.format(
target_dir=target_dir, output=output, prefix=prefix)
run_stage(self.state, 'hmmcopy', command)
def delly(self, input, output, cpu=6):
'''
run the delly singularity container
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
# nothing to do for normal sample
if normal_id is None:
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
# it's a tumour
tmp_id = 'delly-{}-{}'.format(tumour_id, str(uuid.uuid4()))
tmp_dir = '{tmp}/{tmp_id}'.format(tmp=config.TMP, tmp_id=tmp_id)
safe_make_dir(tmp_dir)
with open('{tmp_dir}/delly.sh'.format(tmp_dir=tmp_dir),
'w') as analyse_fh:
for line in open(
'{root}/src/util/delly.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('CORES', str(cpu), new_line)
analyse_fh.write(new_line)
command = 'singularity exec -i --bind {in_dir}:/mnt/in,{out}:/mnt/out,{reference}:/mnt/reference,{tmp_dir}:/mnt/tmp --workdir {tmp_dir} --contain {root}/img/delly-2.0.0.img bash /mnt/tmp/delly.sh 1>{prefix}.delly.log.out 2>{prefix}.delly.log.err && mv {tmp_dir}/workdir {prefix}.delly.results && touch "{output}" && rm -r "{tmp_dir}"'.format(
root=config.ROOT,
in_dir=config.IN,
out=config.OUT,
reference=config.REFERENCE_DELLY,
tmp=config.TMP,
tmp_dir=tmp_dir,
tmp_id=tmp_id,
prefix=prefix,
output=output)
run_stage(self.state, 'delly', command)
def somatic_sniper(self, input, output):
'''
run somatic sniper
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{root}/cfg/sample-metadata.csv".format(root=config.ROOT),
'r'))
# nothing to do for normal sample
if normal_id is None:
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
# it's a tumour
with open(
'{tmp_dir}/{tumour_id}.somatic_sniper.sh'.format(
tmp_dir=config.TMP, tumour_id=tumour_id),
'w') as analyse_fh:
for line in open(
'{root}/src/util/somatic_sniper.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR_ID', tumour_id, line)
new_line = re.sub('NORMAL_ID', normal_id, new_line)
new_line = re.sub('ROOT_PATH', config.ROOT, new_line)
analyse_fh.write(new_line)
command = 'bash {tmp_dir}/{tumour_id}.somatic_sniper.sh 2>{prefix}.somatic_sniper.log.err 1>{prefix}.somatic_sniper.log.out && touch "{output}"'.format(
tmp_dir=config.TMP,
tumour_id=tumour_id,
output=output,
prefix=prefix)
run_stage(self.state, 'somatic_sniper', command)
def gridss(self, input, output):
'''
run gridss
'''
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
# nothing to do for normal sample
if normal_id is None:
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
# it's a tumour
tmp_id = 'gridss-{}-{}'.format(tumour_id, str(uuid.uuid4()))
tmp_dir = '{tmp}/{tmp_id}'.format(tmp=config.TMP, tmp_id=tmp_id)
safe_make_dir(tmp_dir)
with open('{tmp_dir}/gridss.sh'.format(tmp_dir=tmp_dir),
'w') as analyse_fh:
for line in open(
'{root}/src/util/gridss.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
new_line = re.sub('ACCOUNT', config.ACCOUNT, new_line)
analyse_fh.write(new_line)
#command = 'bash {tmp_dir}/muse.sh && touch "{output}" && rm -r "{tmp_dir}"'.format(tmp_dir=tmp_dir, output=output)
command = 'bash {tmp_dir}/gridss.sh 2>{prefix}.gridss.log.err 1>{prefix}.gridss.log.out && touch "{output}" && rm -r {tmp_dir}'.format(
tmp_dir=tmp_dir, output=output, prefix=prefix)
run_stage(self.state, 'gridss', command)
def muse(self, input, output):
'''
run muse
'''
interval = 50000000 # chunk size to break chromosomes into for muse
prefix = re.sub('.mapped.bam$', '',
input) # full path without mapped.bam
tumour_id = prefix.split('/')[-1] # e.g. CMHS1
normal_id = util.find_normal(
tumour_id,
open("{}/cfg/sample-metadata.csv".format(config.ROOT), 'r'))
# nothing to do for normal sample
if normal_id is None:
safe_make_dir(os.path.dirname(output))
with open(output, 'w') as output_fh:
output_fh.write(
'Normal sample does not require analysis. See the relevant tumour file.\n'
)
return
# it's a tumour
tmp_id = 'muse-{}-{}'.format(tumour_id, str(uuid.uuid4()))
tmp_dir = '{tmp}/{tmp_id}'.format(tmp=config.TMP, tmp_id=tmp_id)
safe_make_dir(tmp_dir)
# build combine variants commands
muse_commands = []
cmd = ['samtools', 'view', '-H', input]
proc = subprocess.Popen(cmd, stdout=subprocess.PIPE)
for line in proc.stdout.readlines():
if line.startswith('@SQ\t'):
fields = line.strip().split('\t')
chromosome = fields[1].split(':')[1] # SN
size = int(fields[2].split(':')[1]) # LN
# now write regions as zero based
current = 0
while current < size:
final = min(size, current + interval)
muse_commands.append(
'$MUSE call -O {tmp_dir}/tmp{chromosome}_{current}_{final} -f $REFERENCE -r "{chromosome}:{current}-{final}" $TMR_ABS $NRML_ABS'
.format(tmp_dir=tmp_dir,
chromosome=chromosome,
current=current,
final=final,
prefix=prefix))
current = final
with open('{tmp_dir}/muse.sh'.format(tmp_dir=tmp_dir),
'w') as analyse_fh:
for line in open(
'{root}/src/util/muse.sh.template'.format(
root=config.ROOT), 'r'):
new_line = re.sub('TUMOUR', tumour_id, line)
new_line = re.sub('NORMAL', normal_id, new_line)
new_line = re.sub('TMP_DIR', tmp_dir, new_line)
new_line = re.sub('ROOT', config.ROOT, new_line)
new_line = re.sub('CALL_VARIANTS', '\n'.join(muse_commands),
new_line)
analyse_fh.write(new_line)
#command = 'bash {tmp_dir}/muse.sh && touch "{output}" && rm -r "{tmp_dir}"'.format(tmp_dir=tmp_dir, output=output)
command = 'bash {tmp_dir}/muse.sh 2>{prefix}.muse.log.err 1>{prefix}.muse.log.out && touch "{output}" && rm -r {tmp_dir}'.format(
tmp_dir=tmp_dir, output=output, prefix=prefix)
run_stage(self.state, 'muse', command)