def _run_qsignature_generator(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
:param bam_file: (str) path of the bam_file
:param data: (list) list containing the all the dictionary
for this sample
:param out_dir: (str) path of the output
:returns: (dict) dict with the normalize vcf file
"""
position = dd.get_qsig_file(data)
mixup_check = dd.get_mixup_check(data)
if mixup_check and mixup_check.startswith("qsignature"):
if not position:
logger.info("There is no qsignature for this species: %s" %
tz.get_in(['genome_build'], data))
return {}
jvm_opts = "-Xms750m -Xmx2g"
limit_reads = 20000000
if mixup_check == "qsignature_full":
slice_bam = bam_file
jvm_opts = "-Xms750m -Xmx8g"
limit_reads = 100000000
else:
slice_bam = _slice_chr22(bam_file, data)
qsig = config_utils.get_program("qsignature", data["config"])
if not qsig:
return {}
utils.safe_makedir(out_dir)
out_name = os.path.basename(slice_bam).replace("bam", "qsig.vcf")
out_file = os.path.join(out_dir, out_name)
log_file = os.path.join(out_dir, "qsig.log")
cores = dd.get_cores(data)
base_cmd = ("{qsig} {jvm_opts} "
"org.qcmg.sig.SignatureGenerator "
"--noOfThreads {cores} "
"-log {log_file} -i {position} "
"-i {down_file} ")
if not os.path.exists(out_file):
down_file = bam.downsample(slice_bam, data, limit_reads)
if not down_file:
down_file = slice_bam
file_qsign_out = "{0}.qsig.vcf".format(down_file)
do.run(base_cmd.format(**locals()),
"qsignature vcf generation: %s" % data["name"][-1])
if os.path.exists(file_qsign_out):
with file_transaction(data, out_file) as file_txt_out:
shutil.move(file_qsign_out, file_txt_out)
else:
raise IOError("File doesn't exist %s" % file_qsign_out)
return {'qsig_vcf': out_file}
return {}
def run(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
:param bam_file: (str) path of the bam_file
:param data: (list) list containing the all the dictionary
for this sample
:param out_dir: (str) path of the output
:returns: (string) output normalized vcf file
"""
qsig = config_utils.get_program("qsignature", data["config"])
res_qsig = config_utils.get_resources("qsignature", data["config"])
jvm_opts = " ".join(res_qsig.get("jvm_opts", ["-Xms750m", "-Xmx8g"]))
if not qsig:
logger.info("There is no qsignature tool. Skipping...")
return None
position = dd.get_qsig_file(data)
mixup_check = dd.get_mixup_check(data)
if mixup_check and mixup_check.startswith("qsignature"):
utils.safe_makedir(out_dir)
if not position:
logger.info("There is no qsignature for this species: %s" %
tz.get_in(['genome_build'], data))
return None
if mixup_check == "qsignature_full":
down_bam = bam_file
else:
down_bam = _slice_bam_chr21(bam_file, data)
position = _slice_vcf_chr21(position, out_dir)
out_name = os.path.basename(down_bam).replace("bam", "qsig.vcf")
out_file = os.path.join(out_dir, out_name)
log_file = os.path.join(out_dir, "qsig.log")
cores = dd.get_cores(data)
base_cmd = ("{qsig} {jvm_opts} "
"org.qcmg.sig.SignatureGenerator "
"--noOfThreads {cores} "
"-log {log_file} -i {position} "
"-i {down_bam} ")
if not os.path.exists(out_file):
file_qsign_out = "{0}.qsig.vcf".format(down_bam)
do.run(base_cmd.format(**locals()),
"qsignature vcf generation: %s" % dd.get_sample_name(data))
if os.path.exists(file_qsign_out):
with file_transaction(data, out_file) as file_txt_out:
shutil.move(file_qsign_out, file_txt_out)
else:
raise IOError("File doesn't exist %s" % file_qsign_out)
return out_file
return None
def _run_qsignature_generator(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
:param bam_file: (str) path of the bam_file
:param data: (list) list containing the all the dictionary
for this sample
:param out_dir: (str) path of the output
:returns: (dict) dict with the normalize vcf file
"""
position = dd.get_qsig_file(data)
mixup_check = dd.get_mixup_check(data)
if mixup_check and mixup_check.startswith("qsignature"):
if not position:
logger.info("There is no qsignature for this species: %s"
% tz.get_in(['genome_build'], data))
return {}
jvm_opts = "-Xms750m -Xmx2g"
limit_reads = 20000000
if mixup_check == "qsignature_full":
slice_bam = bam_file
jvm_opts = "-Xms750m -Xmx8g"
limit_reads = 100000000
else:
slice_bam = _slice_chr22(bam_file, data)
qsig = config_utils.get_program("qsignature", data["config"])
if not qsig:
return {}
utils.safe_makedir(out_dir)
out_name = os.path.basename(slice_bam).replace("bam", "qsig.vcf")
out_file = os.path.join(out_dir, out_name)
log_file = os.path.join(out_dir, "qsig.log")
cores = dd.get_cores(data)
base_cmd = ("{qsig} {jvm_opts} "
"org.qcmg.sig.SignatureGenerator "
"--noOfThreads {cores} "
"-log {log_file} -i {position} "
"-i {down_file} ")
if not os.path.exists(out_file):
down_file = bam.downsample(slice_bam, data, limit_reads)
if not down_file:
down_file = slice_bam
file_qsign_out = "{0}.qsig.vcf".format(down_file)
do.run(base_cmd.format(**locals()), "qsignature vcf generation: %s" % data["name"][-1])
if os.path.exists(file_qsign_out):
with file_transaction(data, out_file) as file_txt_out:
shutil.move(file_qsign_out, file_txt_out)
else:
raise IOError("File doesn't exist %s" % file_qsign_out)
return {'qsig_vcf': out_file}
return {}
def run(bam_file, data, out_dir):
""" Run SignatureGenerator to create normalize vcf that later will be input of qsignature_summary
:param bam_file: (str) path of the bam_file
:param data: (list) list containing the all the dictionary
for this sample
:param out_dir: (str) path of the output
:returns: (string) output normalized vcf file
"""
qsig = config_utils.get_program("qsignature", data["config"])
res_qsig = config_utils.get_resources("qsignature", data["config"])
jvm_opts = " ".join(res_qsig.get("jvm_opts", ["-Xms750m", "-Xmx8g"]))
if not qsig:
logger.info("There is no qsignature tool. Skipping...")
return None
position = dd.get_qsig_file(data)
mixup_check = dd.get_mixup_check(data)
if mixup_check and mixup_check.startswith("qsignature"):
utils.safe_makedir(out_dir)
if not position:
logger.info("There is no qsignature for this species: %s"
% tz.get_in(['genome_build'], data))
return None
if mixup_check == "qsignature_full":
down_bam = bam_file
else:
down_bam = _slice_bam_chr21(bam_file, data)
position = _slice_vcf_chr21(position, out_dir)
out_name = os.path.basename(down_bam).replace("bam", "qsig.vcf")
out_file = os.path.join(out_dir, out_name)
log_file = os.path.join(out_dir, "qsig.log")
cores = dd.get_cores(data)
base_cmd = ("{qsig} {jvm_opts} "
"org.qcmg.sig.SignatureGenerator "
"--noOfThreads {cores} "
"-log {log_file} -i {position} "
"-i {down_bam} ")
if not os.path.exists(out_file):
file_qsign_out = "{0}.qsig.vcf".format(down_bam)
do.run(base_cmd.format(**locals()), "qsignature vcf generation: %s" % dd.get_sample_name(data))
if os.path.exists(file_qsign_out):
with file_transaction(data, out_file) as file_txt_out:
shutil.move(file_qsign_out, file_txt_out)
else:
raise IOError("File doesn't exist %s" % file_qsign_out)
return out_file
return None
def _parse_qsignature_output(in_file, out_file, warning_file, data):
""" Parse xml file produced by qsignature
:param in_file: (str) with the path to the xml file
:param out_file: (str) with the path to output file
:param warning_file: (str) with the path to warning file
:returns: (list) with samples that could be duplicated
"""
import lxml
name = {}
error, warnings, similar = set(), set(), set()
same, replicate, related = 0, 0.1, 0.18
mixup_check = dd.get_mixup_check(data)
if mixup_check == "qsignature_full":
same, replicate, related = 0, 0.01, 0.061
with open(in_file, 'r') as in_handle:
with file_transaction(data, out_file) as out_tx_file:
with file_transaction(data, warning_file) as warn_tx_file:
with open(out_tx_file, 'w') as out_handle:
with open(warn_tx_file, 'w') as warn_handle:
et = lxml.etree.parse(in_handle)
for i in list(et.iter('file')):
name[i.attrib['id']] = os.path.basename(
i.attrib['name']).replace(".qsig.vcf", "")
for i in list(et.iter('comparison')):
msg = None
pair = "-".join([
name[i.attrib['file1']],
name[i.attrib['file2']]
])
out_handle.write(
"%s\t%s\t%s\n" %
(name[i.attrib['file1']],
name[i.attrib['file2']], i.attrib['score']))
if float(i.attrib['score']) == same:
msg = 'qsignature ERROR: read same samples:%s\n'
error.add(pair)
elif float(i.attrib['score']) < replicate:
msg = 'qsignature WARNING: read similar/replicate samples:%s\n'
warnings.add(pair)
elif float(i.attrib['score']) < related:
msg = 'qsignature NOTE: read relative samples:%s\n'
similar.add(pair)
if msg:
logger.info(msg % pair)
warn_handle.write(msg % pair)
return error, warnings, similar
def _parse_qsignature_output(in_file, out_file, warning_file, data):
""" Parse xml file produced by qsignature
:param in_file: (str) with the path to the xml file
:param out_file: (str) with the path to output file
:param warning_file: (str) with the path to warning file
:returns: (list) with samples that could be duplicated
"""
name = {}
error, warnings, similar = set(), set(), set()
same, replicate, related = 0, 0.1, 0.18
mixup_check = dd.get_mixup_check(data)
if mixup_check == "qsignature_full":
same, replicate, related = 0, 0.01, 0.061
with open(in_file, 'r') as in_handle:
with file_transaction(data, out_file) as out_tx_file:
with file_transaction(data, warning_file) as warn_tx_file:
with open(out_tx_file, 'w') as out_handle:
with open(warn_tx_file, 'w') as warn_handle:
et = lxml.etree.parse(in_handle)
for i in list(et.iter('file')):
name[i.attrib['id']] = os.path.basename(i.attrib['name']).replace(".qsig.vcf", "")
for i in list(et.iter('comparison')):
msg = None
pair = "-".join([name[i.attrib['file1']], name[i.attrib['file2']]])
out_handle.write("%s\t%s\t%s\n" %
(name[i.attrib['file1']], name[i.attrib['file2']], i.attrib['score']))
if float(i.attrib['score']) == same:
msg = 'qsignature ERROR: read same samples:%s\n'
error.add(pair)
elif float(i.attrib['score']) < replicate:
msg = 'qsignature WARNING: read similar/replicate samples:%s\n'
warnings.add(pair)
elif float(i.attrib['score']) < related:
msg = 'qsignature NOTE: read relative samples:%s\n'
similar.add(pair)
if msg:
logger.info(msg % pair)
warn_handle.write(msg % pair)
return error, warnings, similar
