def main():
parser = argparse.ArgumentParser("Haplotype Comparison")
# input
parser.add_argument("-v",
"--version",
dest="version",
action="store_true",
help="Show version number and exit.")
parser.add_argument("-r",
"--reference",
dest="ref",
default=None,
help="Specify a reference file.")
# output
parser.add_argument("-o",
"--report-prefix",
dest="reports_prefix",
default=None,
help="Filename prefix for report output.")
parser.add_argument("--scratch-prefix",
dest="scratch_prefix",
default=None,
help="Directory for scratch files.")
parser.add_argument("--keep-scratch",
dest="delete_scratch",
default=True,
action="store_false",
help="Filename prefix for scratch report output.")
# add quantification args
qfy.updateArgs(parser)
# control preprocessing
pre.updateArgs(parser)
parser.add_argument(
'--convert-gvcf-truth',
dest='convert_gvcf_truth',
action="store_true",
default=False,
help=
'Convert the truth set from genome VCF format to a VCF before processing.'
)
parser.add_argument(
'--convert-gvcf-query',
dest='convert_gvcf_query',
action="store_true",
default=False,
help=
'Convert the query set from genome VCF format to a VCF before processing.'
)
parser.add_argument(
"--preprocess-truth",
dest="preprocessing_truth",
action="store_true",
default=False,
help=
"Preprocess truth file with same settings as query (default is to accept truth in original format)."
)
parser.add_argument(
"--usefiltered-truth",
dest="usefiltered_truth",
action="store_true",
default=False,
help=
"Use filtered variant calls in truth file (by default, only PASS calls in the truth file are used)"
)
parser.add_argument(
"--preprocessing-window-size",
dest="preprocess_window",
default=10000,
type=int,
help=
"Preprocessing window size (variants further apart than that size are not expected to interfere)."
)
parser.add_argument(
"--adjust-conf-regions",
dest="preprocessing_truth_confregions",
action="store_true",
default=True,
help=
"Adjust confident regions to include variant locations. Note this will only include variants "
"that are included in the CONF regions already when viewing with bcftools; this option only "
"makes sure insertions are padded correctly in the CONF regions (to capture these, both the "
"base before and after must be contained in the bed file).")
parser.add_argument("--no-adjust-conf-regions",
dest="preprocessing_truth_confregions",
action="store_false",
help="Do not adjust confident regions for insertions.")
# detailed control of comparison
parser.add_argument(
"--unhappy",
"--no-haplotype-comparison",
dest="no_hc",
action="store_true",
default=False,
help=
"Disable haplotype comparison (only count direct GT matches as TP).")
parser.add_argument(
"-w",
"--window-size",
dest="window",
default=50,
type=int,
help=
"Minimum distance between variants such that they fall into the same superlocus."
)
# xcmp-specific stuff
parser.add_argument(
"--xcmp-enumeration-threshold",
dest="max_enum",
default=16768,
type=int,
help=
"Enumeration threshold / maximum number of sequences to enumerate per block."
)
parser.add_argument(
"--xcmp-expand-hapblocks",
dest="hb_expand",
default=30,
type=int,
help="Expand haplotype blocks by this many basepairs left and right.")
parser.add_argument("--threads",
dest="threads",
default=multiprocessing.cpu_count(),
type=int,
help="Number of threads to use.")
parser.add_argument(
"--engine",
dest="engine",
default="xcmp",
choices=["xcmp", "vcfeval", "scmp-somatic", "scmp-distance"],
help="Comparison engine to use.")
parser.add_argument(
"--engine-vcfeval-path",
dest="engine_vcfeval",
required=False,
default=Haplo.vcfeval.findVCFEval(),
help="This parameter should give the path to the \"rtg\" executable. "
"The default is %s" % Haplo.vcfeval.findVCFEval())
parser.add_argument(
"--engine-vcfeval-template",
dest="engine_vcfeval_template",
required=False,
help=
"Vcfeval needs the reference sequence formatted in its own file format "
"(SDF -- run rtg format -o ref.SDF ref.fa). You can specify this here "
"to save time when running hap.py with vcfeval. If no SDF folder is "
"specified, hap.py will create a temporary one.")
parser.add_argument(
"--scmp-distance",
dest="engine_scmp_distance",
required=False,
default=30,
type=int,
help=
"For distance-based matching (vcfeval and scmp), this is the distance between variants to use."
)
parser.add_argument(
"--lose-match-distance",
dest="engine_scmp_distance",
required=False,
type=int,
help=
"For distance-based matching (vcfeval and scmp), this is the distance between variants to use."
)
if Tools.has_sge:
parser.add_argument(
"--force-interactive",
dest="force_interactive",
default=False,
action="store_true",
help=
"Force running interactively (i.e. when JOB_ID is not in the environment)"
)
parser.add_argument("_vcfs", help="Two VCF files.", default=[], nargs="*")
parser.add_argument(
"--logfile",
dest="logfile",
default=None,
help="Write logging information into file rather than to stderr")
verbosity_options = parser.add_mutually_exclusive_group(required=False)
verbosity_options.add_argument(
"--verbose",
dest="verbose",
default=False,
action="store_true",
help="Raise logging level from warning to info.")
verbosity_options.add_argument(
"--quiet",
dest="quiet",
default=False,
action="store_true",
help="Set logging level to output errors only.")
args, unknown_args = parser.parse_known_args()
if not Tools.has_sge:
args.force_interactive = True
if args.verbose:
loglevel = logging.INFO
elif args.quiet:
loglevel = logging.ERROR
else:
loglevel = logging.WARNING
# reinitialize logging
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=args.logfile,
format='%(asctime)s %(levelname)-8s %(message)s',
level=loglevel)
# remove some safe unknown args
unknown_args = [
x for x in unknown_args if x not in ["--force-interactive"]
]
if len(sys.argv) < 2 or len(unknown_args) > 0:
if unknown_args:
logging.error("Unknown arguments specified : %s " %
str(unknown_args))
parser.print_help()
exit(1)
print "Hap.py %s" % Tools.version
if args.version:
exit(0)
if args.roc:
args.write_vcf = True
# sanity-check regions bed file (HAP-57)
if args.regions_bedfile:
logging.info("Checking input regions.")
if bedOverlapCheck(args.regions_bedfile):
raise Exception(
"The regions bed file (specified using -R) has overlaps, this will not work with xcmp."
" You can either use -T, or run the file through bedtools merge"
)
if args.fp_bedfile and not os.path.exists(args.fp_bedfile):
raise Exception("FP/confident call region bed file does not exist.")
if not args.force_interactive and "JOB_ID" not in os.environ:
parser.print_help()
raise Exception(
"Please qsub me so I get approximately 1 GB of RAM per thread.")
if not args.ref:
args.ref = Tools.defaultReference()
if not args.ref or not os.path.exists(args.ref):
raise Exception("Please specify a valid reference path using -r.")
if not args.reports_prefix:
raise Exception("Please specify an output prefix using -o ")
if not os.path.exists(os.path.dirname(os.path.abspath(
args.reports_prefix))):
raise Exception(
"The output path does not exist. Please specify a valid output path and prefix using -o"
)
if os.path.basename(args.reports_prefix) == "" or os.path.isdir(
args.reports_prefix):
raise Exception(
"The output path should specify a file name prefix. Please specify a valid output path "
"and prefix using -o. For example, -o /tmp/test will create files named /tmp/test* ."
)
# noinspection PyProtectedMember
if not args._vcfs or len(args._vcfs) != 2:
raise Exception("Please specify exactly two input VCFs.")
# noinspection PyProtectedMember
args.vcf1 = args._vcfs[0]
# noinspection PyProtectedMember
args.vcf2 = args._vcfs[1]
if not os.path.exists(args.vcf1):
raise Exception("Input file %s does not exist." % args.vcf1)
if not os.path.exists(args.vcf2):
raise Exception("Input file %s does not exist." % args.vcf2)
tempfiles = []
# turn on allele conversion
if (args.engine == "scmp-somatic" or args.engine == "scmp-distance") \
and not args.somatic_allele_conversion:
args.somatic_allele_conversion = True
if args.engine == "scmp-distance":
args.somatic_allele_conversion = "first"
# somatic allele conversion should also switch off decomposition
if args.somatic_allele_conversion and ("-D" not in sys.argv
and "--decompose" not in sys.argv):
args.preprocessing_decompose = False
# xcmp/scmp support bcf; others don't
if args.engine in ["xcmp", "scmp-somatic", "scmp-distance"] \
and (args.bcf or (args.vcf1.endswith(".bcf") and args.vcf2.endswith(".bcf"))):
internal_format_suffix = ".bcf"
else:
internal_format_suffix = ".vcf.gz"
# write session info and args file
session = sessionInfo()
session["final_args"] = args.__dict__
with open(args.reports_prefix + ".runinfo.json", "w") as sessionfile:
json.dump(session, sessionfile)
try:
logging.info("Comparing %s and %s" % (args.vcf1, args.vcf2))
logging.info("Preprocessing truth: %s" % args.vcf1)
starttime = time.time()
ttf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.pp",
suffix=internal_format_suffix)
ttf.close()
if args.engine.endswith("somatic") and \
args.preprocessing_truth and \
(args.preprocessing_leftshift or args.preprocessing_norm or args.preprocessing_decompose):
args.preprocessing_truth = False
logging.info(
"Turning off pre.py preprocessing for somatic comparisons")
if args.preprocessing_truth:
if args.filter_nonref:
logging.info(
"Filtering out any variants genotyped as <NON_REF>")
## Only converting truth gvcf to vcf if both arguments are true
convert_gvcf_truth = False
if args.convert_gvcf_truth or args.convert_gvcf_to_vcf:
logging.info("Converting genome VCF to VCF")
convert_gvcf_truth = True
tempfiles.append(ttf.name)
tempfiles.append(ttf.name + ".csi")
tempfiles.append(ttf.name + ".tbi")
args.gender = pre.preprocess(
args.vcf1,
ttf.name,
args.ref,
args.locations,
None if args.usefiltered_truth else "*", # filters
args.fixchr,
args.regions_bedfile,
args.targets_bedfile,
args.preprocessing_leftshift
if args.preprocessing_truth else False,
args.preprocessing_decompose
if args.preprocessing_truth else False,
args.preprocessing_norm if args.preprocessing_truth else False,
args.preprocess_window,
args.threads,
args.gender,
args.somatic_allele_conversion,
"TRUTH",
filter_nonref=args.filter_nonref
if args.preprocessing_truth else False,
convert_gvcf_to_vcf=convert_gvcf_truth)
args.vcf1 = ttf.name
if args.fp_bedfile and args.preprocessing_truth_confregions:
conf_temp = Haplo.gvcf2bed.gvcf2bed(args.vcf1, args.ref,
args.fp_bedfile,
args.scratch_prefix)
tempfiles.append(conf_temp)
args.strat_regions.append("CONF_VARS:" + conf_temp)
h1 = vcfextract.extractHeadersJSON(args.vcf1)
elapsed = time.time() - starttime
logging.info("preprocess for %s -- time taken %.2f" %
(args.vcf1, elapsed))
# once we have preprocessed the truth file we can resolve the locations
# doing this here improves the time for query preprocessing below
reference_contigs = set(fastaContigLengths(args.ref).keys())
if not args.locations:
# default set of locations is the overlap between truth and reference
args.locations = list(reference_contigs
& set(h1["tabix"]["chromosomes"]))
if not args.locations:
raise Exception(
"Truth and reference have no chromosomes in common!")
elif type(args.locations) is not list:
args.locations = args.locations.split(",")
args.locations = sorted(args.locations)
logging.info("Preprocessing query: %s" % args.vcf2)
if args.filter_nonref:
logging.info("Filtering out any variants genotyped as <NON_REF>")
## Only converting truth gvcf to vcf if both arguments are true
convert_gvcf_query = False
if args.convert_gvcf_query or args.convert_gvcf_to_vcf:
logging.info("Converting genome VCF to VCF")
convert_gvcf_query = True
starttime = time.time()
if args.pass_only:
filtering = "*"
else:
filtering = args.filters_only
qtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.pp",
suffix=internal_format_suffix)
qtf.close()
tempfiles.append(qtf.name)
tempfiles.append(qtf.name + ".csi")
tempfiles.append(qtf.name + ".tbi")
if args.engine.endswith("somatic") and \
(args.preprocessing_leftshift or args.preprocessing_norm or args.preprocessing_decompose):
args.preprocessing_leftshift = False
args.preprocessing_norm = False
args.preprocessing_decompose = False
logging.info(
"Turning off pre.py preprocessing (query) for somatic comparisons"
)
pre.preprocess(
args.vcf2,
qtf.name,
args.ref,
str(",".join(args.locations)),
filtering,
args.fixchr,
args.regions_bedfile,
args.targets_bedfile,
args.preprocessing_leftshift,
args.preprocessing_decompose,
args.preprocessing_norm,
args.preprocess_window,
args.threads,
args.gender, # same gender as truth above
args.somatic_allele_conversion,
"QUERY",
filter_nonref=args.filter_nonref,
convert_gvcf_to_vcf=convert_gvcf_query)
args.vcf2 = qtf.name
h2 = vcfextract.extractHeadersJSON(args.vcf2)
elapsed = time.time() - starttime
logging.info("preprocess for %s -- time taken %.2f" %
(args.vcf2, elapsed))
if not h1["tabix"]:
raise Exception("Truth file is not indexed after preprocesing.")
if not h2["tabix"]:
raise Exception("Query file is not indexed after preprocessing.")
for _xc in args.locations:
if _xc not in h2["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in query!" % _xc)
pool = getPool(args.threads)
if args.threads > 1 and args.engine == "xcmp":
logging.info("Running using %i parallel processes." % args.threads)
# find balanced pieces
# cap parallelism at 64 since otherwise bcftools concat below might run out
# of file handles
args.pieces = min(args.threads, 64)
res = runParallel(pool, Haplo.blocksplit.blocksplitWrapper,
args.locations, args)
if None in res:
raise Exception("One of the blocksplit processes failed.")
tempfiles += res
args.locations = []
for f in res:
with open(f) as fp:
for l in fp:
ll = l.strip().split("\t", 3)
if len(ll) < 3:
continue
xchr = ll[0]
start = int(ll[1]) + 1
end = int(ll[2])
args.locations.append("%s:%i-%i" % (xchr, start, end))
# count variants before normalisation
if "samples" not in h1 or not h1["samples"]:
raise Exception("Cannot read sample names from truth VCF file")
if "samples" not in h2 or not h2["samples"]:
raise Exception("Cannot read sample names from query VCF file")
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="hap.py.result.",
suffix=internal_format_suffix)
tf.close()
tempfiles.append(tf.name)
tempfiles.append(tf.name + ".tbi")
tempfiles.append(tf.name + ".csi")
output_name = tf.name
if args.engine == "xcmp":
# do xcmp
logging.info("Using xcmp for comparison")
res = runParallel(pool, Haplo.xcmp.xcmpWrapper, args.locations,
args)
tempfiles += [x for x in res if x is not None] # VCFs
if None in res:
raise Exception("One of the xcmp jobs failed.")
if len(res) == 0:
raise Exception(
"Input files/regions do not contain variants (0 haplotype blocks were processed)."
)
# concatenate + index
logging.info("Concatenating variants...")
runme_list = [x for x in res if x is not None]
if len(runme_list) == 0:
raise Exception("No outputs to concatenate!")
logging.info("Concatenating...")
bcftools.concatenateParts(output_name, *runme_list)
logging.info("Indexing...")
bcftools.runBcftools("index", output_name)
# passed to quantify
args.type = "xcmp"
# xcmp extracts whichever field we're using into the QQ info field
args.roc_header = args.roc
args.roc = "IQQ"
elif args.engine == "vcfeval":
tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2,
output_name, args)
# passed to quantify
args.type = "ga4gh"
elif args.engine.startswith("scmp"):
tempfiles += Haplo.scmp.runSCmp(args.vcf1, args.vcf2, output_name,
args)
# passed to quantify
args.type = "ga4gh"
else:
raise Exception("Unknown comparison engine: %s" % args.engine)
if args.preserve_info and args.engine == "vcfeval":
# if we use vcfeval we need to merge the INFO fields back in.
tf = tempfile.NamedTemporaryFile(suffix=".txt", delete=False)
tempfiles.append(tf)
print >> tf, "TRUTH_IN"
print >> tf, "QUERY_IN"
tf.close()
info_file = tempfile.NamedTemporaryFile(suffix=".vcf.gz",
delete=False)
tempfiles.append(info_file.name)
info_file.close()
bcftools.runBcftools("merge", args.vcf1, args.vcf2,
"--force-samples", "-m", "all", "|",
"bcftools", "reheader", "-s", tf.name, "|",
"bcftools", "view", "-o", info_file.name,
"-O", "z")
bcftools.runBcftools("index", info_file.name)
merged_info_file = tempfile.NamedTemporaryFile(suffix=".vcf.gz",
delete=False)
tempfiles.append(merged_info_file.name)
merged_info_file.close()
bcftools.runBcftools("merge", output_vcf, info_file.name, "-m",
"all", "|", "bcftools", "view", "-s",
"^TRUTH_IN,QUERY_IN", "-X", "-U", "-o",
merged_info_file.name, "-O", "z")
output_name = merged_info_file.name
args.in_vcf = [output_name]
args.runner = "hap.py"
qfy.quantify(args)
finally:
if args.delete_scratch:
for x in tempfiles:
try:
os.remove(x)
except:
pass
else:
logging.info("Scratch files kept : %s" % (str(tempfiles)))
def main():
parser = argparse.ArgumentParser("Haplotype Comparison")
# input
parser.add_argument('--location', '-l', dest='locations', required=False, default=None,
help='Add a location to the compare list (when not given, will use chr1-22, chrX, chrY).')
parser.add_argument("-v", "--version", dest="version", action="store_true",
help="Show version number and exit.")
parser.add_argument("-P", "--include-nonpass", dest="usefiltered", action="store_true", default=False,
help="Use to include failing query variants in comparison.")
parser.add_argument("--include-nonpass-truth", dest="usefiltered_truth", action="store_true", default=False,
help="Include failing variants from the truth dataset.")
parser.add_argument("-R", "--restrict-regions", dest="regions_bedfile",
default=None, type=str,
help="Restrict analysis to given (sparse) regions (using -R in bcftools).")
parser.add_argument("-T", "--target-regions", dest="targets_bedfile",
default=None, type=str,
help="Restrict analysis to given (dense) regions (using -T in bcftools).")
parser.add_argument("-f", "--false-positives", dest="fp_bedfile",
default=None, type=str,
help="False positive / confident call regions (.bed or .bed.gz).")
parser.add_argument("-r", "--reference", dest="ref", default=None, help="Specify a reference file.")
# output
parser.add_argument("-o", "--report-prefix", dest="reports_prefix",
default=None,
help="Filename prefix for report output.")
parser.add_argument("-V", "--write-vcf", dest="write_vcf",
default=False, action="store_true",
help="Write an annotated VCF.")
parser.add_argument("-B", "--write-bed", dest="write_bed",
default=False, action="store_true",
help="Write a bed file with the haplotype blocks that were used.")
parser.add_argument("-X", "--write-counts", dest="write_counts",
default=True, action="store_true",
help="Write advanced counts and metrics.")
parser.add_argument("--no-write-counts", dest="write_counts",
default=True, action="store_false",
help="Do not write advanced counts and metrics.")
parser.add_argument("--raw-counts", dest="raw_counts",
default=False, action="store_true",
help="Count variants in unprocessed input VCFs and output as TOTAL.*.RAW.")
parser.add_argument("--roc", dest="roc", default=False,
help="Select an INFO feature to produce a ROC on. This works best with "
"--no-internal-preprocessing and --no-internal-leftshift since these "
"flags preserve the most INFO flags from the input files.")
parser.add_argument("--roc-filter", dest="roc_filter", default=False,
help="Select a filter to ignore when making ROCs.")
parser.add_argument("--roc-reversed", dest="roc_reversed", default=False,
help="Change the meaning of the ROC feature to count the other way around (higher values=bad).")
parser.add_argument("--scratch-prefix", dest="scratch_prefix",
default=None,
help="Directory for scratch files.")
parser.add_argument("--keep-scratch", dest="delete_scratch",
default=True, action="store_false",
help="Filename prefix for scratch report output.")
# detailed control of comparison
parser.add_argument("--preprocess-truth", dest="preprocessing_truth", action="store_true", default=False,
help="Preprocess truth file using bcftools.")
parser.add_argument("--external-preprocessing", dest="preprocessing", action="store_true", default=False,
help="Perform VCF preprocessing using bcftools.")
parser.add_argument("--bcftools-norm", dest="preprocessing_norm", action="store_true", default=False,
help="Enable preprocessing through bcftools norm -c x -D (requires external "
" preprocessing to be switched on).")
parser.add_argument("--fixchr-truth", dest="fixchr_truth", action="store_true", default=None,
help="Add chr prefix to truth file (default: auto).")
parser.add_argument("--fixchr-query", dest="fixchr_query", action="store_true", default=None,
help="Add chr prefix to query file (default: auto).")
parser.add_argument("--no-fixchr-truth", dest="fixchr_truth", action="store_false",
help="Disable chr replacement for truth (default: auto).")
parser.add_argument("--no-fixchr-query", dest="fixchr_query", action="store_false",
help="Add chr prefix to query file (default: auto).")
parser.add_argument("--partial-credit", dest="partial_credit", action="store_true", default=None,
help="give credit for partially matched variants. "
"this is equivalent to --internal-leftshift and --internal-preprocessing.")
parser.add_argument("--no-partial-credit", dest="partial_credit", action="store_false", default=None,
help="Give credit for partially matched variants. "
"This is equivalent to --internal-leftshift and --no-internal-preprocessing.")
parser.add_argument("--internal-leftshift", dest="int_preprocessing_ls", action="store_true", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--internal-preprocessing", dest="int_preprocessing", action="store_true", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--no-internal-leftshift", dest="int_preprocessing_ls", action="store_false", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--no-internal-preprocessing", dest="int_preprocessing", action="store_false", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--match-raw", dest="int_match_raw", action="store_true", default=False,
help="Add a matching step in xcmp which also matches raw variant calls. This helps"
" when comparing files with very different representations.")
parser.add_argument("--no-haplotype-comparison", dest="no_hc", action="store_true", default=False,
help="Disable haplotype comparison (only count direct GT matches as TP).")
parser.add_argument("--unhappy", dest="unhappy", action="store_true", default=False,
help="Combination of --no-haplotype-comparison --no-internal-preprocessing "
"--no-internal-leftshift.")
parser.add_argument("--no-auto-index", dest="auto_index", action="store_false", default=True,
help="Disable automatic index creation for input files. "
"The index is only necessary at this stage if we want to auto-detect locations. "
"When used with -l, and when it is known that there are variants at all given locations "
"this is not needed and can be switched off to save time.")
parser.add_argument("-w", "--window-size", dest="window",
default=50, type=int,
help="Minimum distance between two variants such that they fall into different haplotype "
"blocks")
parser.add_argument("--enumeration-threshold", dest="max_enum",
default=16768, type=int,
help="Enumeration threshold / maximum number of sequences to enumerate per block.")
parser.add_argument("-e", "--expand-hapblocks", dest="hb_expand",
default=30, type=int,
help="Expand haplotype blocks by this many basepairs left and right.")
parser.add_argument("--threads", dest="threads",
default=multiprocessing.cpu_count(), type=int,
help="Number of threads to use.")
parser.add_argument("--engine", dest="engine",
default="xcmp", choices=["xcmp", "vcfeval"],
help="Comparison engine to use.")
parser.add_argument("--engine-vcfeval-path", dest="engine_vcfeval", required=False,
help="This parameter should give the path to the \"rtg\" executable.")
parser.add_argument("--engine-vcfeval-template", dest="engine_vcfeval_template", required=False,
help="Vcfeval needs the reference sequence formatted in its own file format "
"(SDF -- run rtg format -o ref.SDF ref.fa).")
if Tools.has_sge:
parser.add_argument("--force-interactive", dest="force_interactive",
default=False, action="store_true",
help="Force running interactively (i.e. when JOB_ID is not in the environment)")
parser.add_argument("_vcfs", help="Two VCF files.", default=[], nargs="*")
parser.add_argument("--logfile", dest="logfile", default=None,
help="Write logging information into file rather than to stderr")
verbosity_options = parser.add_mutually_exclusive_group(required=False)
verbosity_options.add_argument("--verbose", dest="verbose", default=False, action="store_true",
help="Raise logging level from warning to info.")
verbosity_options.add_argument("--quiet", dest="quiet", default=False, action="store_true",
help="Set logging level to output errors only.")
args, unknown_args = parser.parse_known_args()
if not Tools.has_sge:
args.force_interactive = True
if args.verbose:
loglevel = logging.INFO
elif args.quiet:
loglevel = logging.ERROR
else:
loglevel = logging.WARNING
# reinitialize logging
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=args.logfile,
format='%(asctime)s %(levelname)-8s %(message)s',
level=loglevel)
# remove some safe unknown args
unknown_args = [x for x in unknown_args if x not in ["--force-interactive"]]
if len(sys.argv) < 2 or len(unknown_args) > 0:
if unknown_args:
logging.error("Unknown arguments specified : %s " % str(unknown_args))
parser.print_help()
exit(0)
if args.version:
print "Hap.py %s" % Tools.version
exit(0)
if args.roc:
args.write_vcf = True
# disable all clever matching
if args.unhappy:
args.int_preprocessing = False
args.int_preprocessing_ls = False
args.no_hc = True
# Counting with partial credit
elif args.partial_credit:
# partial_credit switch is overridden by --no-* switches
args.int_preprocessing = True
args.int_preprocessing_ls = True
elif args.partial_credit is None:
# in the default setting, we enable partial credit but only override the
# preprocessing settings if they haven't been specified
if args.int_preprocessing is None:
args.int_preprocessing = True
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = True
elif args.partial_credit is not None: # explicitly set to false
args.int_preprocessing = False
args.int_preprocessing_ls = True
if args.int_preprocessing is None:
args.int_preprocessing = False
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = False
logging.info("Preprocessing settings: %s / %s / %s" % ("leftshift" if args.int_preprocessing_ls else "no-leftshift",
"splitting" if args.int_preprocessing else "raw calls",
"haplocompare" if not args.no_hc else "no-haplocompare"))
# sanity-check regions bed file (HAP-57)
if args.regions_bedfile:
logging.info("Checking input regions.")
if bedOverlapCheck(args.regions_bedfile):
raise Exception("The regions bed file (specified using -R) has overlaps, this will not work with xcmp."
" You can either use -T, or run the file through bedtools merge")
args.preprocessing_truth = True
args.preprocessing = True
if args.targets_bedfile or args.engine != "xcmp":
args.preprocessing_truth = True
args.preprocessing = True
if args.fp_bedfile and not os.path.exists(args.fp_bedfile):
raise Exception("FP/confident call region bed file does not exist.")
tempfiles = []
try:
if not args.force_interactive and "JOB_ID" not in os.environ:
parser.print_help()
raise Exception("Please qsub me so I get approximately 1 GB of RAM per thread.")
if not args.ref:
args.ref = Tools.defaultReference()
if not os.path.exists(args.ref):
raise Exception("Please specify a valid reference path using -r.")
if not args.reports_prefix:
raise Exception("Please specify an output prefix using -o ")
if not os.path.exists(os.path.dirname(args.reports_prefix)):
raise Exception("The output path does not exist. Please specify a valid output path and prefix using -o")
if os.path.basename(args.reports_prefix) == "" or os.path.isdir(args.reports_prefix):
raise Exception("The output path should specify a file name prefix. Please specify a valid output path "
"and prefix using -o. For example, -o /tmp/test will create files named /tmp/test* .")
# noinspection PyProtectedMember
if not args._vcfs or len(args._vcfs) != 2:
raise Exception("Please specify exactly two input VCFs.")
# noinspection PyProtectedMember
args.vcf1 = args._vcfs[0]
# noinspection PyProtectedMember
args.vcf2 = args._vcfs[1]
if not os.path.exists(args.vcf1):
raise Exception("Input file %s does not exist." % args.vcf1)
if not os.path.exists(args.vcf2):
raise Exception("Input file %s does not exist." % args.vcf2)
logging.info("Comparing %s and %s" % (args.vcf1, args.vcf2))
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.auto_index and not h1["tabix"]:
logging.info("Creating indexed version of %s -- consider creating an index beforehand to save time here." %
args.vcf1)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf1 = Tools.bcftools.makeIndex(args.vcf1, vtf.name)
h1 = vcfextract.extractHeadersJSON(args.vcf1)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if args.auto_index and not h2["tabix"]:
logging.info("Creating indexed version of %s -- consider creating an index beforehand to save time here." %
args.vcf2)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf2 = Tools.bcftools.makeIndex(args.vcf2, vtf.name)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
ref_check = False
try:
happy_ref = args.ref
v1r = [_h for _h in h1["fields"] if _h["key"] == "reference"]
v2r = [_h for _h in h2["fields"] if _h["key"] == "reference"]
if args.verbose:
logging.info("References used: hap.py: %s / truth: %s / "
"query: %s" % (str(happy_ref), str(v1r), str(v2r)))
v1_ref = ";".join([str(xxy["value"]) for xxy in v1r]).replace("file://", "")
v2_ref = ";".join([str(xxy["value"]) for xxy in v2r]).replace("file://", "")
if happy_ref == v1_ref and v1_ref == v2_ref:
ref_check = True
refids_found = 0
for refid in ["hg19", "hg38", "grc37", "grc38"]:
if refid in happy_ref.lower() and refid in v1_ref.lower() and refid in v2_ref.lower():
if args.verbose:
logging.info("Reference matches pattern: %s" % refid)
refids_found += 1
if refids_found == 1:
ref_check = True
except:
pass
if not ref_check:
logging.warn("Reference sequence check failed! "
"Please ensure that truth and query VCF use the same reference sequence as "
"hap.py. XCMP may fail if this is not the case, and the results will not be "
" accurate.")
if args.locations is None or len(args.locations) == 0:
# all chromosomes
args.locations = ["chr" + x for x in map(str, range(1, 23))]
if type(args.locations) is not list and args.locations is not None:
# noinspection PyUnresolvedReferences
args.locations = args.locations.split(",")
if not h1["tabix"]:
args.preprocessing_truth = True
logging.warn("Truth file is not Tabix indexed. Switching on pre-processing + chr name conversion.")
if args.fixchr_truth is None:
args.fixchr_truth = True
elif args.fixchr_truth is None:
# autodetect chr naming
count_with_fix = len([__ for __ in h1["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations])
count_no_fix = len([__ for __ in h1["tabix"]["chromosomes"] if str(__) in args.locations])
logging.info("Truth: Number of chromosome names matching with / without renaming : %i / %i " % (
count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_truth = True
logging.info("Will fix chromosome names (truth).")
else:
logging.info("Will not fix chromosome names (truth).")
args.fixchr_truth = False
if not h2["tabix"]:
args.preprocessing = True
logging.warn("Query file is not Tabix indexed. Switching on pre-processing + chr name conversion.")
# don't overwrite setting, but if it's None, replace with True to be sure
if args.fixchr_query is None:
args.fixchr_query = True
elif args.fixchr_query is None:
# autodetect chr naming
count_with_fix = len([__ for __ in h2["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations])
count_no_fix = len([__ for __ in h2["tabix"]["chromosomes"] if str(__) in args.locations])
logging.info("Query: Number of chromosome names matching with / without renaming : %i / %i " % (
count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_query = True
logging.info("Will fix chromosome names (query).")
else:
logging.info("Will not fix chromosome names (query).")
args.fixchr_query = False
if args.fixchr_truth or args.preprocessing_norm:
args.preprocessing_truth = True
if args.fixchr_query or args.preprocessing_norm:
args.preprocessing = True
if args.preprocessing_truth:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(args.vcf1, vtf.name, ",".join(args.locations),
not args.usefiltered_truth, # pass_only
args.fixchr_truth, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf1 = vtf.name
# get headers again if we preprocessed
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.preprocessing:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(args.vcf2, vtf.name, ",".join(args.locations),
not args.usefiltered, # pass_only
args.fixchr_query, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf2 = vtf.name
# get headers again if we preprocessed
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if not h1["tabix"]:
raise Exception("Truth file is not Tabix indexed.")
if not h2["tabix"]:
raise Exception("Truth file is not Tabix indexed.")
newlocations = []
if not h1["tabix"]["chromosomes"]:
h1["tabix"]["chromosomes"] = []
if not h2["tabix"]["chromosomes"]:
h2["tabix"]["chromosomes"] = []
for _xc in args.locations:
xc = _xc.split(":")[0]
if xc not in h1["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in truth!" % xc)
if xc not in h2["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in query!" % xc)
if (xc not in h1["tabix"]["chromosomes"]) and (xc not in h2["tabix"]["chromosomes"]):
logging.warn("Removing location %s because neither input file has calls there." % xc)
else:
newlocations.append(_xc)
if not newlocations:
raise Exception("Location list is empty: the input files do not appear to have variants on any of %s" %
str(args.locations))
args.locations = newlocations
if args.threads > 1:
logging.info("Running using %i parallel processes." % args.threads)
pool = multiprocessing.Pool(int(args.threads))
# find balanced pieces
args.pieces = (args.threads + len(args.locations) - 1) / len(args.locations)
res = runParallel(pool, Haplo.blocksplit.blocksplitWrapper, args.locations, args)
if None in res:
raise Exception("One of the blocksplit processes failed.")
tempfiles += res
args.locations = []
for f in res:
with open(f) as fp:
for l in fp:
ll = l.strip().split("\t", 3)
if len(ll) < 3:
continue
xchr = ll[0]
start = int(ll[1]) + 1
end = int(ll[2])
args.locations.append("%s:%i-%i" % (xchr, start, end))
else:
pool = None
# count variants before normalisation
if "samples" not in h1 or not h1["samples"]:
raise Exception("Cannot read sample names from truth input file")
if args.raw_counts:
counts_truth = Haplo.quantify.run_quantify(args.vcf1,
None,
None,
{"CONF": args.fp_bedfile} if args.fp_bedfile else None,
args.ref,
h1["samples"][0],
locations=args.locations)
else:
counts_truth = None
if "samples" not in h2 or not h2["samples"]:
raise Exception("Cannot read sample names from truth input file")
if args.raw_counts:
counts_query = Haplo.quantify.run_quantify(args.vcf2,
None,
None,
{"CONF": args.fp_bedfile} if args.fp_bedfile else None,
args.ref,
h2["samples"][0],
locations=args.locations)
else:
counts_query = None
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="hap.py.result.", suffix=".vcf.gz")
tf.close()
tempfiles.append(tf.name)
output_name = tf.name
if args.engine == "xcmp":
# do xcmp
logging.info("Using xcmp for comparison")
res = runParallel(pool, Haplo.xcmp.xcmpWrapper, args.locations, args)
tempfiles += [x[0] for x in res if x is not None] # VCFs
tempfiles += [x[1] for x in res if x is not None and x[1] is not None] # beds (if any)
if None in res:
raise Exception("One of the xcmp jobs failed.")
if len(res) == 0:
raise Exception("Input files/regions do not contain variants (0 haplotype blocks were processed).")
# concatenate + index
bedfiles = [x[1] for x in res if x is not None and x[1] is not None]
if args.write_bed and bedfiles:
runme = " ".join(["cat"] +
bedfiles +
[">", args.reports_prefix.replace(" ", "\\ ") + ".blocks.bed"])
logging.info("Concatenating block files: %s..." % runme)
subprocess.check_call(runme,
shell=True)
logging.info("Concatenating variants...")
runme_list = [x[0] for x in res if x is not None]
if len(runme_list) == 0:
raise Exception("No outputs to concatenate!")
fo = Tools.BGZipFile(output_name, True)
for i, x in enumerate(runme_list):
f = gzip.GzipFile(x)
for l in f:
if i == 0 or not l[0] == "#":
fo.write(l)
fo.close()
logging.info("Indexing...")
to_run = "tabix -p vcf %s" % output_name.replace(" ", "\\ ")
logging.info("Running '%s'" % to_run)
subprocess.check_call(to_run, shell=True)
elif args.engine == "vcfeval":
tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2, output_name, args)
else:
raise Exception("Unknown comparison engine: %s" % args.engine)
if args.write_counts:
json_name = args.reports_prefix + ".counts.json"
else:
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="counts.",
suffix=".json")
tf.close()
json_name = tf.name
logging.info("Counting variants...")
counts = Haplo.quantify.run_quantify(output_name,
json_name,
args.reports_prefix + ".vcf.gz" if args.write_vcf else False,
{"CONF": args.fp_bedfile} if args.fp_bedfile else None,
args.ref)
df = pandas.DataFrame(counts)
if args.write_counts:
df.to_csv(args.reports_prefix + ".counts.csv")
metrics_output = makeMetricsObject("hap.py.comparison")
if args.write_counts:
metrics_output["metrics"].append(dataframeToMetricsTable("raw.counts", df))
# calculate precision / recall
count_types = []
if args.raw_counts:
simplified_truth_counts = Haplo.quantify.simplify_counts(counts_truth, h1["samples"][0:1])
simplified_query_counts = Haplo.quantify.simplify_counts(counts_query, h2["samples"][0:1])
count_types += simplified_truth_counts.keys()
count_types += simplified_query_counts.keys()
else:
simplified_truth_counts = None
simplified_query_counts = None
simplified_numbers = Haplo.quantify.simplify_counts(counts)
count_types += simplified_numbers.keys()
count_types = sorted(list(set(count_types)))
for vtype in count_types:
if vtype not in simplified_numbers:
simplified_numbers[vtype] = {}
simplified_numbers[vtype]["METRIC.Recall"] = 0
simplified_numbers[vtype]["METRIC.Recall2"] = 0
simplified_numbers[vtype]["METRIC.Precision"] = 0
simplified_numbers[vtype]["METRIC.Frac_NA"] = 0
try:
simplified_numbers[vtype]["METRIC.Recall"] = \
float(simplified_numbers[vtype]["TRUTH.TP"]) / \
float(simplified_numbers[vtype]["TRUTH.TP"] + simplified_numbers[vtype]["TRUTH.FN"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Recall2"] = \
float(simplified_numbers[vtype]["TRUTH.TP"]) / \
float(simplified_numbers[vtype]["TRUTH.TOTAL"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Precision"] = \
float(simplified_numbers[vtype]["QUERY.TP"]) / \
float(simplified_numbers[vtype]["QUERY.TP"] + simplified_numbers[vtype]["QUERY.FP"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Frac_NA"] = \
float(simplified_numbers[vtype]["QUERY.UNK"]) / \
float(simplified_numbers[vtype]["QUERY.TOTAL"])
except:
pass
try:
simplified_numbers[vtype]["TRUTH.TOTAL.RAW"] = simplified_truth_counts[vtype][h1["samples"][0] +
".TOTAL"]
except:
pass
try:
simplified_numbers[vtype]["QUERY.TOTAL.RAW"] = simplified_query_counts[vtype][h2["samples"][0] +
".TOTAL"]
except:
pass
pandas.set_option("display.width", 120)
pandas.set_option("display.max_columns", 1000)
df = pandas.DataFrame(simplified_numbers).transpose()
vstring = "hap.py-%s" % Tools.version
vstring += " ".join(sys.argv)
df.loc[vstring] = 0
# for x in df:
# # everything not a metric is a count
# if not x.startswith("METRIC"):
# df[x] = df[x].astype("int64")
df[["TRUTH.TOTAL",
"QUERY.TOTAL",
"METRIC.Recall",
"METRIC.Precision",
"METRIC.Frac_NA"]].to_csv(args.reports_prefix + ".summary.csv")
metrics_output["metrics"].append(dataframeToMetricsTable("summary.metrics",
df[["TRUTH.TOTAL",
"QUERY.TOTAL",
"METRIC.Recall",
"METRIC.Precision",
"METRIC.Frac_NA"]]))
if args.write_counts:
df.to_csv(args.reports_prefix + ".extended.csv")
metrics_output["metrics"].append(dataframeToMetricsTable("all.metrics", df))
essential_numbers = df[["TRUTH.TOTAL",
"QUERY.TOTAL",
"METRIC.Recall",
"METRIC.Precision",
"METRIC.Frac_NA"]]
pandas.set_option('display.max_columns', 500)
pandas.set_option('display.width', 1000)
essential_numbers = essential_numbers[essential_numbers.index.isin(
["Locations.SNP", "Locations.INDEL"])]
logging.info("\n" + str(essential_numbers))
# in default mode, print result summary to stdout
if not args.quiet and not args.verbose:
print "Benchmarking Summary:"
print str(essential_numbers)
if args.roc:
vcf = args.reports_prefix + ".vcf.gz"
res = Haplo.happyroc.roc(vcf, args.roc, args.roc_filter, args.reports_prefix + ".roc", args.roc_reversed)
for t in res.iterkeys():
rocdf = pandas.read_table(res[t])
metrics_output["metrics"].append(dataframeToMetricsTable("roc." + t, rocdf))
with open(args.reports_prefix + ".metrics.json", "w") as fp:
json.dump(metrics_output, fp)
finally:
if args.delete_scratch:
for x in tempfiles:
try:
os.remove(x)
except:
pass
else:
logging.info("Scratch files kept : %s" % (str(tempfiles)))
def main():
parser = argparse.ArgumentParser("Haplotype Comparison")
# input
parser.add_argument("-v", "--version", dest="version", action="store_true",
help="Show version number and exit.")
parser.add_argument("-r", "--reference", dest="ref", default=None, help="Specify a reference file.")
# output
parser.add_argument("-o", "--report-prefix", dest="reports_prefix",
default=None,
help="Filename prefix for report output.")
parser.add_argument("--scratch-prefix", dest="scratch_prefix",
default=None,
help="Directory for scratch files.")
parser.add_argument("--keep-scratch", dest="delete_scratch",
default=True, action="store_false",
help="Filename prefix for scratch report output.")
# add quantification args
qfy.updateArgs(parser)
# control preprocessing
pre.updateArgs(parser)
parser.add_argument("--preprocess-truth", dest="preprocessing_truth", action="store_true", default=False,
help="Preprocess truth file with same settings as query (default is to accept truth in original format).")
parser.add_argument("--usefiltered-truth", dest="usefiltered_truth", action="store_true", default=False,
help="Preprocess truth file with same settings as query (default is to accept truth in original format).")
parser.add_argument("--preprocessing-window-size", dest="preprocess_window",
default=10000, type=int,
help="Preprocessing window size (variants further apart than that size are not expected to interfere).")
# detailed control of comparison
parser.add_argument("--unhappy", "--no-haplotype-comparison", dest="no_hc", action="store_true", default=False,
help="Disable haplotype comparison (only count direct GT matches as TP).")
parser.add_argument("-w", "--window-size", dest="window",
default=50, type=int,
help="Minimum distance between variants such that they fall into the same superlocus.")
# xcmp-specific stuff
parser.add_argument("--xcmp-enumeration-threshold", dest="max_enum",
default=16768, type=int,
help="Enumeration threshold / maximum number of sequences to enumerate per block.")
parser.add_argument("--xcmp-expand-hapblocks", dest="hb_expand",
default=30, type=int,
help="Expand haplotype blocks by this many basepairs left and right.")
parser.add_argument("--threads", dest="threads",
default=multiprocessing.cpu_count(), type=int,
help="Number of threads to use.")
parser.add_argument("--engine", dest="engine",
default="xcmp", choices=["xcmp", "vcfeval"],
help="Comparison engine to use.")
parser.add_argument("--engine-vcfeval-path", dest="engine_vcfeval", required=False,
default=Haplo.vcfeval.findVCFEval(),
help="This parameter should give the path to the \"rtg\" executable. "
"The default is %s" % Haplo.vcfeval.findVCFEval())
parser.add_argument("--engine-vcfeval-template", dest="engine_vcfeval_template", required=False,
help="Vcfeval needs the reference sequence formatted in its own file format "
"(SDF -- run rtg format -o ref.SDF ref.fa). You can specify this here "
"to save time when running hap.py with vcfeval. If no SDF folder is "
"specified, hap.py will create a temporary one.")
if Tools.has_sge:
parser.add_argument("--force-interactive", dest="force_interactive",
default=False, action="store_true",
help="Force running interactively (i.e. when JOB_ID is not in the environment)")
parser.add_argument("_vcfs", help="Two VCF files.", default=[], nargs="*")
parser.add_argument("--logfile", dest="logfile", default=None,
help="Write logging information into file rather than to stderr")
verbosity_options = parser.add_mutually_exclusive_group(required=False)
verbosity_options.add_argument("--verbose", dest="verbose", default=False, action="store_true",
help="Raise logging level from warning to info.")
verbosity_options.add_argument("--quiet", dest="quiet", default=False, action="store_true",
help="Set logging level to output errors only.")
args, unknown_args = parser.parse_known_args()
if not Tools.has_sge:
args.force_interactive = True
if args.verbose:
loglevel = logging.INFO
elif args.quiet:
loglevel = logging.ERROR
else:
loglevel = logging.WARNING
# reinitialize logging
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=args.logfile,
format='%(asctime)s %(levelname)-8s %(message)s',
level=loglevel)
# remove some safe unknown args
unknown_args = [x for x in unknown_args if x not in ["--force-interactive"]]
if len(sys.argv) < 2 or len(unknown_args) > 0:
if unknown_args:
logging.error("Unknown arguments specified : %s " % str(unknown_args))
parser.print_help()
exit(1)
if args.version:
print "Hap.py %s" % Tools.version
exit(0)
if args.roc:
args.write_vcf = True
# sanity-check regions bed file (HAP-57)
if args.regions_bedfile:
logging.info("Checking input regions.")
if bedOverlapCheck(args.regions_bedfile):
raise Exception("The regions bed file (specified using -R) has overlaps, this will not work with xcmp."
" You can either use -T, or run the file through bedtools merge")
if args.fp_bedfile and not os.path.exists(args.fp_bedfile):
raise Exception("FP/confident call region bed file does not exist.")
if not args.force_interactive and "JOB_ID" not in os.environ:
parser.print_help()
raise Exception("Please qsub me so I get approximately 1 GB of RAM per thread.")
if not args.ref:
args.ref = Tools.defaultReference()
if not os.path.exists(args.ref):
raise Exception("Please specify a valid reference path using -r.")
if not args.reports_prefix:
raise Exception("Please specify an output prefix using -o ")
if not os.path.exists(os.path.dirname(os.path.abspath(args.reports_prefix))):
raise Exception("The output path does not exist. Please specify a valid output path and prefix using -o")
if os.path.basename(args.reports_prefix) == "" or os.path.isdir(args.reports_prefix):
raise Exception("The output path should specify a file name prefix. Please specify a valid output path "
"and prefix using -o. For example, -o /tmp/test will create files named /tmp/test* .")
# noinspection PyProtectedMember
if not args._vcfs or len(args._vcfs) != 2:
raise Exception("Please specify exactly two input VCFs.")
# noinspection PyProtectedMember
args.vcf1 = args._vcfs[0]
# noinspection PyProtectedMember
args.vcf2 = args._vcfs[1]
if not os.path.exists(args.vcf1):
raise Exception("Input file %s does not exist." % args.vcf1)
if not os.path.exists(args.vcf2):
raise Exception("Input file %s does not exist." % args.vcf2)
tempfiles = []
# xcmp supports bcf; others don't
if args.engine == "xcmp" and (args.bcf or (args.vcf1.endswith(".bcf") and args.vcf2.endswith(".bcf"))):
internal_format_suffix = ".bcf"
else:
internal_format_suffix = ".vcf.gz"
try:
logging.info("Comparing %s and %s" % (args.vcf1, args.vcf2))
logging.info("Preprocessing truth: %s" % args.vcf1)
starttime = time.time()
ttf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.pp",
suffix=internal_format_suffix)
ttf.close()
tempfiles.append(ttf.name)
tempfiles.append(ttf.name + ".csi")
tempfiles.append(ttf.name + ".tbi")
pre.preprocess(args.vcf1,
ttf.name,
args.ref,
args.locations,
None if args.usefiltered_truth else "*", # filters
args.fixchr,
args.regions_bedfile,
args.targets_bedfile,
args.preprocessing_leftshift if args.preprocessing_truth else False,
args.preprocessing_decompose if args.preprocessing_truth else False,
args.preprocessing_norm if args.preprocessing_truth else False,
args.preprocess_window,
args.threads)
args.vcf1 = ttf.name
h1 = vcfextract.extractHeadersJSON(args.vcf1)
elapsed = time.time() - starttime
logging.info("preprocess for %s -- time taken %.2f" % (args.vcf1, elapsed))
# once we have preprocessed the truth file we can resolve the locations
# doing this here improves the time for query preprocessing below
reference_contigs = set(fastaContigLengths(args.ref).keys())
if not args.locations:
# default set of locations is the overlap between truth and reference
args.locations = list(reference_contigs & set(h1["tabix"]["chromosomes"]))
if not args.locations:
raise Exception("Truth and reference have no chromosomes in common!")
elif type(args.locations) is not list:
args.locations = [args.locations]
args.locations = sorted(args.locations)
logging.info("Preprocessing query: %s" % args.vcf2)
starttime = time.time()
if args.pass_only:
filtering = "*"
else:
filtering = args.filters_only
qtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.pp",
suffix=internal_format_suffix)
qtf.close()
tempfiles.append(qtf.name)
tempfiles.append(qtf.name + ".csi")
tempfiles.append(qtf.name + ".tbi")
pre.preprocess(args.vcf2,
qtf.name,
args.ref,
str(",".join(args.locations)),
filtering,
args.fixchr,
args.regions_bedfile,
args.targets_bedfile,
args.preprocessing_leftshift,
args.preprocessing_decompose,
args.preprocessing_norm,
args.preprocess_window,
args.threads)
args.vcf2 = qtf.name
h2 = vcfextract.extractHeadersJSON(args.vcf2)
elapsed = time.time() - starttime
logging.info("preprocess for %s -- time taken %.2f" % (args.vcf2, elapsed))
if not h1["tabix"]:
raise Exception("Truth file is not indexed after preprocesing.")
if not h2["tabix"]:
raise Exception("Query file is not indexed after preprocessing.")
for _xc in args.locations:
if _xc not in h2["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in query!" % _xc)
pool = getPool(args.threads)
if args.threads > 1 and args.engine == "xcmp":
logging.info("Running using %i parallel processes." % args.threads)
# find balanced pieces
# cap parallelism at 64 since otherwise bcftools concat below might run out
# of file handles
args.pieces = min(args.threads, 64)
res = runParallel(pool, Haplo.blocksplit.blocksplitWrapper, args.locations, args)
if None in res:
raise Exception("One of the blocksplit processes failed.")
tempfiles += res
args.locations = []
for f in res:
with open(f) as fp:
for l in fp:
ll = l.strip().split("\t", 3)
if len(ll) < 3:
continue
xchr = ll[0]
start = int(ll[1]) + 1
end = int(ll[2])
args.locations.append("%s:%i-%i" % (xchr, start, end))
# count variants before normalisation
if "samples" not in h1 or not h1["samples"]:
raise Exception("Cannot read sample names from truth VCF file")
if "samples" not in h2 or not h2["samples"]:
raise Exception("Cannot read sample names from query VCF file")
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="hap.py.result.",
suffix=internal_format_suffix)
tf.close()
tempfiles.append(tf.name)
tempfiles.append(tf.name + ".tbi")
tempfiles.append(tf.name + ".csi")
output_name = tf.name
if args.engine == "xcmp":
# do xcmp
logging.info("Using xcmp for comparison")
res = runParallel(pool, Haplo.xcmp.xcmpWrapper, args.locations, args)
tempfiles += [x for x in res if x is not None] # VCFs
if None in res:
raise Exception("One of the xcmp jobs failed.")
if len(res) == 0:
raise Exception("Input files/regions do not contain variants (0 haplotype blocks were processed).")
# concatenate + index
logging.info("Concatenating variants...")
runme_list = [x for x in res if x is not None]
if len(runme_list) == 0:
raise Exception("No outputs to concatenate!")
logging.info("Concatenating...")
bcftools.concatenateParts(output_name, *runme_list)
logging.info("Indexing...")
bcftools.runBcftools("index", output_name)
# passed to quantify
args.type = "xcmp"
# xcmp extracts whichever field we're using into the QQ info field
args.roc = "IQQ"
elif args.engine == "vcfeval":
tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2, output_name, args)
# passed to quantify
args.type = "ga4gh"
else:
raise Exception("Unknown comparison engine: %s" % args.engine)
args.in_vcf = [output_name]
args.runner = "hap.py"
qfy.quantify(args)
finally:
if args.delete_scratch:
for x in tempfiles:
try:
os.remove(x)
except:
pass
else:
logging.info("Scratch files kept : %s" % (str(tempfiles)))
def main():
parser = argparse.ArgumentParser("Haplotype Comparison")
# input
parser.add_argument('--location', '-l', dest='locations', required=False, default=None,
help='Add a location to the compare list (when not given, will use chr1-22, chrX, chrY).')
parser.add_argument("-v", "--version", dest="version", action="store_true",
help="Show version number and exit.")
parser.add_argument("-P", "--include-nonpass", dest="usefiltered", action="store_true", default=False,
help="Use to include failing query variants in comparison.")
parser.add_argument("--include-nonpass-truth", dest="usefiltered_truth", action="store_true", default=False,
help="Include failing variants from the truth dataset.")
parser.add_argument("-R", "--restrict-regions", dest="regions_bedfile",
default=None, type=str,
help="Restrict analysis to given (sparse) regions (using -R in bcftools).")
parser.add_argument("-T", "--target-regions", dest="targets_bedfile",
default=None, type=str,
help="Restrict analysis to given (dense) regions (using -T in bcftools).")
parser.add_argument("-r", "--reference", dest="ref", default=None, help="Specify a reference file.")
# output
parser.add_argument("-o", "--report-prefix", dest="reports_prefix",
default=None,
help="Filename prefix for report output.")
# DEPRECATED: we don't write bed files after 0.2.9
parser.add_argument("-B", "--write-bed", dest="write_bed",
default=False, action="store_true",
help="This option is deprecated. BED files will not be written anymore.")
# add quantification args
qfy.updateArgs(parser)
parser.add_argument("--scratch-prefix", dest="scratch_prefix",
default=None,
help="Directory for scratch files.")
parser.add_argument("--keep-scratch", dest="delete_scratch",
default=True, action="store_false",
help="Filename prefix for scratch report output.")
# detailed control of comparison
parser.add_argument("--preprocess-truth", dest="preprocessing_truth", action="store_true", default=False,
help="Preprocess truth file using bcftools.")
parser.add_argument("--external-preprocessing", dest="preprocessing", action="store_true", default=False,
help="Perform VCF preprocessing using bcftools.")
parser.add_argument("--bcftools-norm", dest="preprocessing_norm", action="store_true", default=False,
help="Enable preprocessing through bcftools norm -c x -D (requires external "
" preprocessing to be switched on).")
parser.add_argument("-N", "--numeric-chromosomes", dest="numeric_chrs", action="store_true", default=None,
help="Use numeric chromosome names for truth and query. This is a shortcut for "
"-l 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y "
"--no-fixchr-truth --no-fixchr-query")
parser.add_argument("-C", "--no-numeric-chromosomes", dest="numeric_chrs", action="store_false",
help="Use chr-prefixed chromosome names for truth and query. This is a shortcut for "
"-l chr1,...,chrY"
"--fixchr-truth --fixchr-query")
parser.add_argument("--fixchr-truth", dest="fixchr_truth", action="store_true", default=None,
help="Add chr prefix to truth file (default: auto).")
parser.add_argument("--fixchr-query", dest="fixchr_query", action="store_true", default=None,
help="Add chr prefix to query file (default: auto).")
parser.add_argument("--no-fixchr-truth", dest="fixchr_truth", action="store_false",
help="Disable chr replacement for truth (default: auto).")
parser.add_argument("--no-fixchr-query", dest="fixchr_query", action="store_false",
help="Add chr prefix to query file (default: auto).")
parser.add_argument("--partial-credit", dest="partial_credit", action="store_true", default=None,
help="give credit for partially matched variants. "
"this is equivalent to --internal-leftshift and --internal-preprocessing.")
parser.add_argument("--no-partial-credit", dest="partial_credit", action="store_false", default=None,
help="Give credit for partially matched variants. "
"This is equivalent to --internal-leftshift and --no-internal-preprocessing.")
parser.add_argument("--internal-leftshift", dest="int_preprocessing_ls", action="store_true", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--internal-preprocessing", dest="int_preprocessing", action="store_true", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--no-internal-leftshift", dest="int_preprocessing_ls", action="store_false", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--no-internal-preprocessing", dest="int_preprocessing", action="store_false", default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument("--no-haplotype-comparison", dest="no_hc", action="store_true", default=False,
help="Disable haplotype comparison (only count direct GT matches as TP).")
parser.add_argument("--unhappy", dest="unhappy", action="store_true", default=False,
help="Combination of --no-haplotype-comparison --no-internal-preprocessing "
"--no-internal-leftshift.")
parser.add_argument("--no-auto-index", dest="auto_index", action="store_false", default=True,
help="Disable automatic index creation for input files. "
"The index is only necessary at this stage if we want to auto-detect locations. "
"When used with -l, and when it is known that there are variants at all given locations "
"this is not needed and can be switched off to save time.")
parser.add_argument("-w", "--window-size", dest="window",
default=50, type=int,
help="Minimum distance between two variants such that they fall into different haplotype "
"blocks")
parser.add_argument("--enumeration-threshold", dest="max_enum",
default=16768, type=int,
help="Enumeration threshold / maximum number of sequences to enumerate per block.")
parser.add_argument("-e", "--expand-hapblocks", dest="hb_expand",
default=30, type=int,
help="Expand haplotype blocks by this many basepairs left and right.")
parser.add_argument("--threads", dest="threads",
default=multiprocessing.cpu_count(), type=int,
help="Number of threads to use.")
parser.add_argument("--engine", dest="engine",
default="xcmp", choices=["xcmp", "vcfeval"],
help="Comparison engine to use.")
parser.add_argument("--engine-vcfeval-path", dest="engine_vcfeval", required=False,
help="This parameter should give the path to the \"rtg\" executable.")
parser.add_argument("--engine-vcfeval-template", dest="engine_vcfeval_template", required=False,
help="Vcfeval needs the reference sequence formatted in its own file format "
"(SDF -- run rtg format -o ref.SDF ref.fa).")
if Tools.has_sge:
parser.add_argument("--force-interactive", dest="force_interactive",
default=False, action="store_true",
help="Force running interactively (i.e. when JOB_ID is not in the environment)")
parser.add_argument("_vcfs", help="Two VCF files.", default=[], nargs="*")
parser.add_argument("--logfile", dest="logfile", default=None,
help="Write logging information into file rather than to stderr")
verbosity_options = parser.add_mutually_exclusive_group(required=False)
verbosity_options.add_argument("--verbose", dest="verbose", default=False, action="store_true",
help="Raise logging level from warning to info.")
verbosity_options.add_argument("--quiet", dest="quiet", default=False, action="store_true",
help="Set logging level to output errors only.")
args, unknown_args = parser.parse_known_args()
if not Tools.has_sge:
args.force_interactive = True
if args.verbose:
loglevel = logging.INFO
elif args.quiet:
loglevel = logging.ERROR
else:
loglevel = logging.WARNING
# reinitialize logging
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=args.logfile,
format='%(asctime)s %(levelname)-8s %(message)s',
level=loglevel)
# remove some safe unknown args
unknown_args = [x for x in unknown_args if x not in ["--force-interactive"]]
if len(sys.argv) < 2 or len(unknown_args) > 0:
if unknown_args:
logging.error("Unknown arguments specified : %s " % str(unknown_args))
parser.print_help()
exit(0)
if args.version:
print "Hap.py %s" % Tools.version
exit(0)
if args.write_bed:
logging.warn("The -B / --write-bed switches are deprecated in versions 0.2.9+, ")
if args.roc:
args.write_vcf = True
# disable all clever matching
if args.unhappy:
args.int_preprocessing = False
args.int_preprocessing_ls = False
args.no_hc = True
# Counting with partial credit
elif args.partial_credit:
# partial_credit switch is overridden by --no-* switches
args.int_preprocessing = True
args.int_preprocessing_ls = True
elif args.partial_credit is None:
# in the default setting, we enable partial credit but only override the
# preprocessing settings if they haven't been specified
if args.int_preprocessing is None:
args.int_preprocessing = True
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = True
elif args.partial_credit is not None: # explicitly set to false
args.int_preprocessing = False
args.int_preprocessing_ls = True
if args.int_preprocessing is None:
args.int_preprocessing = False
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = False
logging.info("Preprocessing settings: %s / %s / %s" % ("leftshift" if args.int_preprocessing_ls else "no-leftshift",
"splitting" if args.int_preprocessing else "raw calls",
"haplocompare" if not args.no_hc else "no-haplocompare"))
# sanity-check regions bed file (HAP-57)
if args.regions_bedfile:
logging.info("Checking input regions.")
if bedOverlapCheck(args.regions_bedfile):
raise Exception("The regions bed file (specified using -R) has overlaps, this will not work with xcmp."
" You can either use -T, or run the file through bedtools merge")
args.preprocessing_truth = True
args.preprocessing = True
if args.targets_bedfile or args.engine != "xcmp":
args.preprocessing_truth = True
args.preprocessing = True
if args.fp_bedfile and not os.path.exists(args.fp_bedfile):
raise Exception("FP/confident call region bed file does not exist.")
tempfiles = []
try:
if not args.force_interactive and "JOB_ID" not in os.environ:
parser.print_help()
raise Exception("Please qsub me so I get approximately 1 GB of RAM per thread.")
if not args.ref:
args.ref = Tools.defaultReference()
if not os.path.exists(args.ref):
raise Exception("Please specify a valid reference path using -r.")
if not args.reports_prefix:
raise Exception("Please specify an output prefix using -o ")
if not os.path.exists(os.path.dirname(os.path.abspath(args.reports_prefix))):
raise Exception("The output path does not exist. Please specify a valid output path and prefix using -o")
if os.path.basename(args.reports_prefix) == "" or os.path.isdir(args.reports_prefix):
raise Exception("The output path should specify a file name prefix. Please specify a valid output path "
"and prefix using -o. For example, -o /tmp/test will create files named /tmp/test* .")
# noinspection PyProtectedMember
if not args._vcfs or len(args._vcfs) != 2:
raise Exception("Please specify exactly two input VCFs.")
# noinspection PyProtectedMember
args.vcf1 = args._vcfs[0]
# noinspection PyProtectedMember
args.vcf2 = args._vcfs[1]
if not os.path.exists(args.vcf1):
raise Exception("Input file %s does not exist." % args.vcf1)
if not os.path.exists(args.vcf2):
raise Exception("Input file %s does not exist." % args.vcf2)
logging.info("Comparing %s and %s" % (args.vcf1, args.vcf2))
# detect numeric chromosome names
if args.numeric_chrs is None:
cts = fastaContigLengths(args.ref)
cts = set(cts.keys())
numeric_names = set(map(str, range(1, 23)) + ["X", "Y", "M"])
non_numeric_names = set(["chr" + x for x in numeric_names])
numeric_names &= cts
non_numeric_names &= cts
numeric_names = len(list(numeric_names))
non_numeric_names = len(list(non_numeric_names))
if numeric_names != 0 and non_numeric_names == 0:
args.numeric_chrs = True
logging.info("Auto-detected numeric chromosome names")
elif numeric_names == 0 and non_numeric_names != 0:
args.numeric_chrs = False
logging.info("Auto-detected chr-prefixed chromosome names")
if args.numeric_chrs:
args.fixchr_truth = False
args.fixchr_query = False
elif args.numeric_chrs is not None:
args.fixchr_truth = True
args.fixchr_query = True
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.auto_index and not h1["tabix"]:
logging.info("Creating indexed version of %s -- consider creating an index beforehand to save time here." %
args.vcf1)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf1 = Tools.bcftools.makeIndex(args.vcf1, vtf.name)
h1 = vcfextract.extractHeadersJSON(args.vcf1)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if args.auto_index and not h2["tabix"]:
logging.info("Creating indexed version of %s -- consider creating an index beforehand to save time here." %
args.vcf2)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf2 = Tools.bcftools.makeIndex(args.vcf2, vtf.name)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
ref_check = True
try:
happy_ref = args.ref
v1r = [_h for _h in h1["fields"] if _h["key"] == "reference"]
v2r = [_h for _h in h2["fields"] if _h["key"] == "reference"]
if args.verbose:
logging.info("References used: hap.py: %s / truth: %s / "
"query: %s" % (str(happy_ref), str(v1r), str(v2r)))
v1_ref = ";".join([str(xxy["value"]) for xxy in v1r]).replace("file://", "")
v2_ref = ";".join([str(xxy["value"]) for xxy in v2r]).replace("file://", "")
if happy_ref == v1_ref and v1_ref == v2_ref:
ref_check = True
rids_vh = set()
rids_v1 = set()
rids_v2 = set()
for refid in ["hg19", "hg38", "grc37", "grc38"]:
if refid in happy_ref.lower():
rids_vh.add(refid)
if refid in v1_ref.lower():
rids_v1.add(refid)
if refid in v2_ref.lower():
rids_v2.add(refid)
rids_v1 = sorted(list(rids_v1))
rids_v2 = sorted(list(rids_v2))
rids_vh = sorted(list(rids_vh))
to_cmp = None
if rids_v1:
to_cmp = rids_v1
if rids_v2:
to_cmp = rids_v2
if rids_vh:
to_cmp = rids_vh
if to_cmp and rids_v1 and rids_v1 != to_cmp:
ref_check = False
if to_cmp and rids_v2 and rids_v2 != to_cmp:
ref_check = False
if to_cmp and rids_vh and rids_vh != to_cmp:
ref_check = False
except:
pass
if not ref_check:
logging.warn("Reference sequence check failed! "
"Please ensure that truth and query VCF use the same reference sequence as "
"hap.py. XCMP may fail if this is not the case, and the results will not be "
" accurate.")
if args.locations is None or len(args.locations) == 0:
# all chromosomes
if args.numeric_chrs:
args.locations = [x for x in map(str, range(1, 23))]
else:
args.locations = ["chr" + x for x in map(str, range(1, 23))]
if type(args.locations) is not list and args.locations is not None:
# noinspection PyUnresolvedReferences
args.locations = args.locations.split(",")
# HAP-143 fix the case where no chromosomes are in truth or query
try:
if not h1["tabix"]["chromosomes"]:
h1["tabix"]["chromosomes"] = []
except:
pass
try:
if not h2["tabix"]["chromosomes"]:
h2["tabix"]["chromosomes"] = []
except:
pass
if not h1["tabix"]:
args.preprocessing_truth = True
logging.warn("Truth file is not Tabix indexed. Switching on pre-processing + chr name conversion.")
if args.fixchr_truth is None:
args.fixchr_truth = True
elif args.fixchr_truth is None:
logging.info(str(h1["tabix"]))
# autodetect chr naming
count_with_fix = len([__ for __ in h1["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations])
count_no_fix = len([__ for __ in h1["tabix"]["chromosomes"] if str(__) in args.locations])
logging.info("Truth: Number of chromosome names matching with / without renaming : %i / %i " % (
count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_truth = True
logging.info("Will fix chromosome names (truth).")
else:
logging.info("Will not fix chromosome names (truth).")
args.fixchr_truth = False
if not h2["tabix"]:
args.preprocessing = True
logging.warn("Query file is not Tabix indexed. Switching on pre-processing + chr name conversion.")
# don't overwrite setting, but if it's None, replace with True to be sure
if args.fixchr_query is None:
args.fixchr_query = True
elif args.fixchr_query is None:
# autodetect chr naming
count_with_fix = len([__ for __ in h2["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations])
count_no_fix = len([__ for __ in h2["tabix"]["chromosomes"] if str(__) in args.locations])
logging.info("Query: Number of chromosome names matching with / without renaming : %i / %i " % (
count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_query = True
logging.info("Will fix chromosome names (query).")
else:
logging.info("Will not fix chromosome names (query).")
args.fixchr_query = False
if args.fixchr_truth or args.preprocessing_norm:
args.preprocessing_truth = True
if args.fixchr_query or args.preprocessing_norm:
args.preprocessing = True
if args.preprocessing_truth:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(args.vcf1, vtf.name, ",".join(args.locations),
not args.usefiltered_truth, # pass_only
args.fixchr_truth, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf1 = vtf.name
# get headers again if we preprocessed
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.preprocessing:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(args.vcf2, vtf.name, ",".join(args.locations),
False, # query filters are handled further down in matching
args.fixchr_query, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf2 = vtf.name
# get headers again if we preprocessed
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if not h1["tabix"]:
raise Exception("Truth file is not Tabix indexed.")
if not h2["tabix"]:
raise Exception("Query file is not Tabix indexed.")
newlocations = []
if not h1["tabix"]["chromosomes"]:
h1["tabix"]["chromosomes"] = []
if not h2["tabix"]["chromosomes"]:
h2["tabix"]["chromosomes"] = []
for _xc in args.locations:
xc = _xc.split(":")[0]
if xc not in h1["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in truth!" % xc)
if xc not in h2["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in query!" % xc)
if (xc not in h1["tabix"]["chromosomes"]) and (xc not in h2["tabix"]["chromosomes"]):
logging.warn("Removing location %s because neither input file has calls there." % xc)
else:
newlocations.append(_xc)
if not newlocations:
raise Exception("Location list is empty: the input files do not appear to have variants on any of %s" %
str(args.locations))
args.locations = newlocations
if args.threads > 1 and args.engine == "xcmp":
logging.info("Running using %i parallel processes." % args.threads)
pool = multiprocessing.Pool(int(args.threads))
# find balanced pieces
args.pieces = (args.threads + len(args.locations) - 1) / len(args.locations)
res = runParallel(pool, Haplo.blocksplit.blocksplitWrapper, args.locations, args)
if None in res:
raise Exception("One of the blocksplit processes failed.")
tempfiles += res
args.locations = []
for f in res:
with open(f) as fp:
for l in fp:
ll = l.strip().split("\t", 3)
if len(ll) < 3:
continue
xchr = ll[0]
start = int(ll[1]) + 1
end = int(ll[2])
args.locations.append("%s:%i-%i" % (xchr, start, end))
else:
pool = None
# count variants before normalisation
if "samples" not in h1 or not h1["samples"]:
raise Exception("Cannot read sample names from truth VCF file")
if "samples" not in h2 or not h2["samples"]:
raise Exception("Cannot read sample names from query VCF file")
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="hap.py.result.", suffix=".vcf.gz")
tf.close()
tempfiles.append(tf.name)
output_name = tf.name
if args.engine == "xcmp":
# do xcmp
logging.info("Using xcmp for comparison")
res = runParallel(pool, Haplo.xcmp.xcmpWrapper, args.locations, args)
tempfiles += [x[0] for x in res if x is not None] # VCFs
tempfiles += [x[1] for x in res if x is not None and x[1] is not None] # beds (if any)
if None in res:
raise Exception("One of the xcmp jobs failed.")
if len(res) == 0:
raise Exception("Input files/regions do not contain variants (0 haplotype blocks were processed).")
# concatenate + index
logging.info("Concatenating variants...")
runme_list = [x[0] for x in res if x is not None]
if len(runme_list) == 0:
raise Exception("No outputs to concatenate!")
fo = Tools.BGZipFile(output_name, True)
for i, x in enumerate(runme_list):
f = gzip.GzipFile(x)
for l in f:
if i == 0 or not l[0] == "#":
fo.write(l)
fo.close()
logging.info("Indexing...")
to_run = "tabix -p vcf %s" % output_name.replace(" ", "\\ ")
logging.info("Running '%s'" % to_run)
subprocess.check_call(to_run, shell=True)
# passed to quantify
args.type = "xcmp"
elif args.engine == "vcfeval":
tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2, output_name, args)
# passed to quantify
args.type = "ga4gh"
else:
raise Exception("Unknown comparison engine: %s" % args.engine)
logging.info("Counting variants...")
args.in_vcf = [output_name]
args.runner = "hap.py"
qfy.quantify(args)
finally:
if args.delete_scratch:
for x in tempfiles:
try:
os.remove(x)
except:
pass
else:
logging.info("Scratch files kept : %s" % (str(tempfiles)))
def partialCredit(vcfname,
outputname,
reference,
locations,
threads=1,
window=10000,
leftshift=True,
decompose=True,
haploid_x=False):
""" Partial-credit-process a VCF file according to our args """
pool = getPool(int(threads))
if threads > 1:
logging.info("Partial credit processing uses %i parallel processes." % threads)
if not locations:
h = extractHeadersJSON(vcfname)
if not h["tabix"]["chromosomes"]:
logging.warn("Empty input or not tabix indexed")
if outputname.endswith(".bcf"):
runBcftools("view", "-O", "b", "-o", outputname, vcfname)
runBcftools("index", outputname)
else:
runBcftools("view", "-O", "z", "-o", outputname, vcfname)
runBcftools("index", "-t", outputname)
# just return the same file
return
locations = h["tabix"]["chromosomes"]
elif type(locations) is str or type(locations) is unicode:
locations = locations.split(",")
# use blocksplit to subdivide input
res = runParallel(pool,
blocksplitWrapper,
locations,
{"vcf": vcfname,
"dist": window,
"pieces": min(40, threads*4)})
if None in res:
raise Exception("One of the blocksplit processes failed.")
locations = list(itertools.chain.from_iterable(res))
if not len(locations):
logging.warn("Blocksplit returned no blocks. This can happen when "
"an input contains no valid variants.")
locations = [""]
else:
locations = [""]
res = []
try:
res = runParallel(pool,
preprocessWrapper,
itertools.izip(itertools.repeat(vcfname), locations),
{"reference": reference,
"decompose": decompose,
"leftshift": leftshift,
"haploid_x": haploid_x,
"bcf": outputname.endswith(".bcf")})
if None in res:
raise Exception("One of the preprocess jobs failed")
if not res:
raise Exception("No blocks were processed. List of locations: %s" % str(list(locations)))
concatenateParts(outputname, *res)
if outputname.endswith(".vcf.gz"):
runBcftools("index", "-f", "-t", outputname)
else: # use bcf
runBcftools("index", "-f", outputname)
finally:
for r in res:
try:
os.unlink(r)
except:
pass
try:
os.unlink(r + ".tbi")
except:
pass
try:
os.unlink(r + ".csi")
except:
pass
def main():
parser = argparse.ArgumentParser("Haplotype Comparison")
# input
parser.add_argument(
'--location',
'-l',
dest='locations',
required=False,
default=None,
help=
'Add a location to the compare list (when not given, will use chr1-22, chrX, chrY).'
)
parser.add_argument("-v",
"--version",
dest="version",
action="store_true",
help="Show version number and exit.")
parser.add_argument(
"-P",
"--include-nonpass",
dest="usefiltered",
action="store_true",
default=False,
help="Use to include failing query variants in comparison.")
parser.add_argument(
"--include-nonpass-truth",
dest="usefiltered_truth",
action="store_true",
default=False,
help="Include failing variants from the truth dataset.")
parser.add_argument(
"-R",
"--restrict-regions",
dest="regions_bedfile",
default=None,
type=str,
help=
"Restrict analysis to given (sparse) regions (using -R in bcftools).")
parser.add_argument(
"-T",
"--target-regions",
dest="targets_bedfile",
default=None,
type=str,
help=
"Restrict analysis to given (dense) regions (using -T in bcftools).")
parser.add_argument(
"-f",
"--false-positives",
dest="fp_bedfile",
default=None,
type=str,
help="False positive / confident call regions (.bed or .bed.gz).")
parser.add_argument("-r",
"--reference",
dest="ref",
default=None,
help="Specify a reference file.")
# output
parser.add_argument("-o",
"--report-prefix",
dest="reports_prefix",
default=None,
help="Filename prefix for report output.")
parser.add_argument("-V",
"--write-vcf",
dest="write_vcf",
default=False,
action="store_true",
help="Write an annotated VCF.")
parser.add_argument(
"-B",
"--write-bed",
dest="write_bed",
default=False,
action="store_true",
help="Write a bed file with the haplotype blocks that were used.")
parser.add_argument("-X",
"--write-counts",
dest="write_counts",
default=True,
action="store_true",
help="Write advanced counts and metrics.")
parser.add_argument("--no-write-counts",
dest="write_counts",
default=True,
action="store_false",
help="Do not write advanced counts and metrics.")
parser.add_argument(
"--raw-counts",
dest="raw_counts",
default=False,
action="store_true",
help=
"Count variants in unprocessed input VCFs and output as TOTAL.*.RAW.")
parser.add_argument(
"--roc",
dest="roc",
default=False,
help="Select an INFO feature to produce a ROC on. This works best with "
"--no-internal-preprocessing and --no-internal-leftshift since these "
"flags preserve the most INFO flags from the input files.")
parser.add_argument("--roc-filter",
dest="roc_filter",
default=False,
help="Select a filter to ignore when making ROCs.")
parser.add_argument(
"--roc-reversed",
dest="roc_reversed",
default=False,
help=
"Change the meaning of the ROC feature to count the other way around (higher values=bad)."
)
parser.add_argument("--scratch-prefix",
dest="scratch_prefix",
default=None,
help="Directory for scratch files.")
parser.add_argument("--keep-scratch",
dest="delete_scratch",
default=True,
action="store_false",
help="Filename prefix for scratch report output.")
# detailed control of comparison
parser.add_argument("--preprocess-truth",
dest="preprocessing_truth",
action="store_true",
default=False,
help="Preprocess truth file using bcftools.")
parser.add_argument("--external-preprocessing",
dest="preprocessing",
action="store_true",
default=False,
help="Perform VCF preprocessing using bcftools.")
parser.add_argument(
"--bcftools-norm",
dest="preprocessing_norm",
action="store_true",
default=False,
help=
"Enable preprocessing through bcftools norm -c x -D (requires external "
" preprocessing to be switched on).")
parser.add_argument("--fixchr-truth",
dest="fixchr_truth",
action="store_true",
default=None,
help="Add chr prefix to truth file (default: auto).")
parser.add_argument("--fixchr-query",
dest="fixchr_query",
action="store_true",
default=None,
help="Add chr prefix to query file (default: auto).")
parser.add_argument(
"--no-fixchr-truth",
dest="fixchr_truth",
action="store_false",
help="Disable chr replacement for truth (default: auto).")
parser.add_argument("--no-fixchr-query",
dest="fixchr_query",
action="store_false",
help="Add chr prefix to query file (default: auto).")
parser.add_argument(
"--partial-credit",
dest="partial_credit",
action="store_true",
default=None,
help="give credit for partially matched variants. "
"this is equivalent to --internal-leftshift and --internal-preprocessing."
)
parser.add_argument(
"--no-partial-credit",
dest="partial_credit",
action="store_false",
default=None,
help="Give credit for partially matched variants. "
"This is equivalent to --internal-leftshift and --no-internal-preprocessing."
)
parser.add_argument(
"--internal-leftshift",
dest="int_preprocessing_ls",
action="store_true",
default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument(
"--internal-preprocessing",
dest="int_preprocessing",
action="store_true",
default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument(
"--no-internal-leftshift",
dest="int_preprocessing_ls",
action="store_false",
default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument(
"--no-internal-preprocessing",
dest="int_preprocessing",
action="store_false",
default=None,
help="Switch off xcmp's internal VCF leftshift preprocessing.")
parser.add_argument(
"--match-raw",
dest="int_match_raw",
action="store_true",
default=False,
help=
"Add a matching step in xcmp which also matches raw variant calls. This helps"
" when comparing files with very different representations.")
parser.add_argument(
"--no-haplotype-comparison",
dest="no_hc",
action="store_true",
default=False,
help=
"Disable haplotype comparison (only count direct GT matches as TP).")
parser.add_argument(
"--unhappy",
dest="unhappy",
action="store_true",
default=False,
help=
"Combination of --no-haplotype-comparison --no-internal-preprocessing "
"--no-internal-leftshift.")
parser.add_argument(
"--no-auto-index",
dest="auto_index",
action="store_false",
default=True,
help="Disable automatic index creation for input files. "
"The index is only necessary at this stage if we want to auto-detect locations. "
"When used with -l, and when it is known that there are variants at all given locations "
"this is not needed and can be switched off to save time.")
parser.add_argument(
"-w",
"--window-size",
dest="window",
default=50,
type=int,
help=
"Minimum distance between two variants such that they fall into different haplotype "
"blocks")
parser.add_argument(
"--enumeration-threshold",
dest="max_enum",
default=16768,
type=int,
help=
"Enumeration threshold / maximum number of sequences to enumerate per block."
)
parser.add_argument(
"-e",
"--expand-hapblocks",
dest="hb_expand",
default=30,
type=int,
help="Expand haplotype blocks by this many basepairs left and right.")
parser.add_argument("--threads",
dest="threads",
default=multiprocessing.cpu_count(),
type=int,
help="Number of threads to use.")
parser.add_argument("--engine",
dest="engine",
default="xcmp",
choices=["xcmp", "vcfeval"],
help="Comparison engine to use.")
parser.add_argument(
"--engine-vcfeval-path",
dest="engine_vcfeval",
required=False,
help="This parameter should give the path to the \"rtg\" executable.")
parser.add_argument(
"--engine-vcfeval-template",
dest="engine_vcfeval_template",
required=False,
help=
"Vcfeval needs the reference sequence formatted in its own file format "
"(SDF -- run rtg format -o ref.SDF ref.fa).")
if Tools.has_sge:
parser.add_argument(
"--force-interactive",
dest="force_interactive",
default=False,
action="store_true",
help=
"Force running interactively (i.e. when JOB_ID is not in the environment)"
)
parser.add_argument("_vcfs", help="Two VCF files.", default=[], nargs="*")
parser.add_argument(
"--logfile",
dest="logfile",
default=None,
help="Write logging information into file rather than to stderr")
verbosity_options = parser.add_mutually_exclusive_group(required=False)
verbosity_options.add_argument(
"--verbose",
dest="verbose",
default=False,
action="store_true",
help="Raise logging level from warning to info.")
verbosity_options.add_argument(
"--quiet",
dest="quiet",
default=False,
action="store_true",
help="Set logging level to output errors only.")
args, unknown_args = parser.parse_known_args()
if not Tools.has_sge:
args.force_interactive = True
if args.verbose:
loglevel = logging.INFO
elif args.quiet:
loglevel = logging.ERROR
else:
loglevel = logging.WARNING
# reinitialize logging
for handler in logging.root.handlers[:]:
logging.root.removeHandler(handler)
logging.basicConfig(filename=args.logfile,
format='%(asctime)s %(levelname)-8s %(message)s',
level=loglevel)
# remove some safe unknown args
unknown_args = [
x for x in unknown_args if x not in ["--force-interactive"]
]
if len(sys.argv) < 2 or len(unknown_args) > 0:
if unknown_args:
logging.error("Unknown arguments specified : %s " %
str(unknown_args))
parser.print_help()
exit(0)
if args.version:
print "Hap.py %s" % Tools.version
exit(0)
if args.roc:
args.write_vcf = True
# disable all clever matching
if args.unhappy:
args.int_preprocessing = False
args.int_preprocessing_ls = False
args.no_hc = True
# Counting with partial credit
elif args.partial_credit:
# partial_credit switch is overridden by --no-* switches
args.int_preprocessing = True
args.int_preprocessing_ls = True
elif args.partial_credit is None:
# in the default setting, we enable partial credit but only override the
# preprocessing settings if they haven't been specified
if args.int_preprocessing is None:
args.int_preprocessing = True
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = True
elif args.partial_credit is not None: # explicitly set to false
args.int_preprocessing = False
args.int_preprocessing_ls = True
if args.int_preprocessing is None:
args.int_preprocessing = False
if args.int_preprocessing_ls is None:
args.int_preprocessing_ls = False
logging.info("Preprocessing settings: %s / %s / %s" %
("leftshift" if args.int_preprocessing_ls else "no-leftshift",
"splitting" if args.int_preprocessing else "raw calls",
"haplocompare" if not args.no_hc else "no-haplocompare"))
# sanity-check regions bed file (HAP-57)
if args.regions_bedfile:
logging.info("Checking input regions.")
if bedOverlapCheck(args.regions_bedfile):
raise Exception(
"The regions bed file (specified using -R) has overlaps, this will not work with xcmp."
" You can either use -T, or run the file through bedtools merge"
)
args.preprocessing_truth = True
args.preprocessing = True
if args.targets_bedfile or args.engine != "xcmp":
args.preprocessing_truth = True
args.preprocessing = True
if args.fp_bedfile and not os.path.exists(args.fp_bedfile):
raise Exception("FP/confident call region bed file does not exist.")
tempfiles = []
try:
if not args.force_interactive and "JOB_ID" not in os.environ:
parser.print_help()
raise Exception(
"Please qsub me so I get approximately 1 GB of RAM per thread."
)
if not args.ref:
args.ref = Tools.defaultReference()
if not os.path.exists(args.ref):
raise Exception("Please specify a valid reference path using -r.")
if not args.reports_prefix:
raise Exception("Please specify an output prefix using -o ")
if not os.path.exists(
os.path.dirname(os.path.abspath(args.reports_prefix))):
raise Exception(
"The output path does not exist. Please specify a valid output path and prefix using -o"
)
if os.path.basename(args.reports_prefix) == "" or os.path.isdir(
args.reports_prefix):
raise Exception(
"The output path should specify a file name prefix. Please specify a valid output path "
"and prefix using -o. For example, -o /tmp/test will create files named /tmp/test* ."
)
# noinspection PyProtectedMember
if not args._vcfs or len(args._vcfs) != 2:
raise Exception("Please specify exactly two input VCFs.")
# noinspection PyProtectedMember
args.vcf1 = args._vcfs[0]
# noinspection PyProtectedMember
args.vcf2 = args._vcfs[1]
if not os.path.exists(args.vcf1):
raise Exception("Input file %s does not exist." % args.vcf1)
if not os.path.exists(args.vcf2):
raise Exception("Input file %s does not exist." % args.vcf2)
logging.info("Comparing %s and %s" % (args.vcf1, args.vcf2))
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.auto_index and not h1["tabix"]:
logging.info(
"Creating indexed version of %s -- consider creating an index beforehand to save time here."
% args.vcf1)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf1 = Tools.bcftools.makeIndex(args.vcf1, vtf.name)
h1 = vcfextract.extractHeadersJSON(args.vcf1)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if args.auto_index and not h2["tabix"]:
logging.info(
"Creating indexed version of %s -- consider creating an index beforehand to save time here."
% args.vcf2)
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.ix",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
tempfiles.append(vtf.name + ".tbi")
args.vcf2 = Tools.bcftools.makeIndex(args.vcf2, vtf.name)
h2 = vcfextract.extractHeadersJSON(args.vcf2)
ref_check = True
try:
happy_ref = args.ref
v1r = [_h for _h in h1["fields"] if _h["key"] == "reference"]
v2r = [_h for _h in h2["fields"] if _h["key"] == "reference"]
if args.verbose:
logging.info("References used: hap.py: %s / truth: %s / "
"query: %s" %
(str(happy_ref), str(v1r), str(v2r)))
v1_ref = ";".join([str(xxy["value"])
for xxy in v1r]).replace("file://", "")
v2_ref = ";".join([str(xxy["value"])
for xxy in v2r]).replace("file://", "")
if happy_ref == v1_ref and v1_ref == v2_ref:
ref_check = True
refids_found = 0
rids_vh = set()
rids_v1 = set()
rids_v2 = set()
for refid in ["hg19", "hg38", "grc37", "grc38"]:
if refid in happy_ref.lower():
rids_vh.add(refid)
if refid in v1_ref.lower():
rids_v1.add(refid)
if refid in v2_ref.lower():
rids_v2.add(refid)
rids_v1 = sorted(list(rids_v1))
rids_v2 = sorted(list(rids_v2))
rids_vh = sorted(list(rids_vh))
to_cmp = None
if rids_v1: to_cmp = rids_v1
if rids_v2: to_cmp = rids_v2
if rids_vh: to_cmp = rids_vh
if to_cmp and rids_v1 and rids_v1 != to_cmp:
ref_check = False
if to_cmp and rids_v2 and rids_v2 != to_cmp:
ref_check = False
if to_cmp and rids_vh and rids_vh != to_cmp:
ref_check = False
except:
pass
if not ref_check:
logging.warn(
"Reference sequence check failed! "
"Please ensure that truth and query VCF use the same reference sequence as "
"hap.py. XCMP may fail if this is not the case, and the results will not be "
" accurate.")
if args.locations is None or len(args.locations) == 0:
# all chromosomes
args.locations = ["chr" + x for x in map(str, range(1, 23))]
if type(args.locations) is not list and args.locations is not None:
# noinspection PyUnresolvedReferences
args.locations = args.locations.split(",")
# HAP-143 fix the case where no chromosomes are in truth or query
try:
if not h1["tabix"]["chromosomes"]:
h1["tabix"]["chromosomes"] = []
except:
pass
try:
if not h2["tabix"]["chromosomes"]:
h2["tabix"]["chromosomes"] = []
except:
pass
if not h1["tabix"]:
args.preprocessing_truth = True
logging.warn(
"Truth file is not Tabix indexed. Switching on pre-processing + chr name conversion."
)
if args.fixchr_truth is None:
args.fixchr_truth = True
elif args.fixchr_truth is None:
logging.info(str(h1["tabix"]))
# autodetect chr naming
count_with_fix = len([
__ for __ in h1["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations
])
count_no_fix = len([
__ for __ in h1["tabix"]["chromosomes"]
if str(__) in args.locations
])
logging.info(
"Truth: Number of chromosome names matching with / without renaming : %i / %i "
% (count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_truth = True
logging.info("Will fix chromosome names (truth).")
else:
logging.info("Will not fix chromosome names (truth).")
args.fixchr_truth = False
if not h2["tabix"]:
args.preprocessing = True
logging.warn(
"Query file is not Tabix indexed. Switching on pre-processing + chr name conversion."
)
# don't overwrite setting, but if it's None, replace with True to be sure
if args.fixchr_query is None:
args.fixchr_query = True
elif args.fixchr_query is None:
# autodetect chr naming
count_with_fix = len([
__ for __ in h2["tabix"]["chromosomes"]
if ("chr%s" % str(__)) in args.locations
])
count_no_fix = len([
__ for __ in h2["tabix"]["chromosomes"]
if str(__) in args.locations
])
logging.info(
"Query: Number of chromosome names matching with / without renaming : %i / %i "
% (count_with_fix, count_no_fix))
if count_with_fix > count_no_fix:
args.fixchr_query = True
logging.info("Will fix chromosome names (query).")
else:
logging.info("Will not fix chromosome names (query).")
args.fixchr_query = False
if args.fixchr_truth or args.preprocessing_norm:
args.preprocessing_truth = True
if args.fixchr_query or args.preprocessing_norm:
args.preprocessing = True
if args.preprocessing_truth:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="truth.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(
args.vcf1,
vtf.name,
",".join(args.locations),
not args.usefiltered_truth, # pass_only
args.fixchr_truth, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf1 = vtf.name
# get headers again if we preprocessed
h1 = vcfextract.extractHeadersJSON(args.vcf1)
if args.preprocessing:
vtf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="query.pp",
suffix=".vcf.gz")
vtf.close()
tempfiles.append(vtf.name)
preprocessVCF(
args.vcf2,
vtf.name,
",".join(args.locations),
not args.usefiltered, # pass_only
args.fixchr_query, # chrprefix
args.preprocessing_norm, # norm,
args.regions_bedfile,
args.targets_bedfile,
args.ref)
args.vcf2 = vtf.name
# get headers again if we preprocessed
h2 = vcfextract.extractHeadersJSON(args.vcf2)
if not h1["tabix"]:
raise Exception("Truth file is not Tabix indexed.")
if not h2["tabix"]:
raise Exception("Query file is not Tabix indexed.")
newlocations = []
if not h1["tabix"]["chromosomes"]:
h1["tabix"]["chromosomes"] = []
if not h2["tabix"]["chromosomes"]:
h2["tabix"]["chromosomes"] = []
for _xc in args.locations:
xc = _xc.split(":")[0]
if xc not in h1["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in truth!" % xc)
if xc not in h2["tabix"]["chromosomes"]:
logging.warn("No calls for location %s in query!" % xc)
if (xc not in h1["tabix"]["chromosomes"]) and (
xc not in h2["tabix"]["chromosomes"]):
logging.warn(
"Removing location %s because neither input file has calls there."
% xc)
else:
newlocations.append(_xc)
if not newlocations:
raise Exception(
"Location list is empty: the input files do not appear to have variants on any of %s"
% str(args.locations))
args.locations = newlocations
if args.threads > 1:
logging.info("Running using %i parallel processes." % args.threads)
pool = multiprocessing.Pool(int(args.threads))
# find balanced pieces
args.pieces = (args.threads + len(args.locations) - 1) / len(
args.locations)
res = runParallel(pool, Haplo.blocksplit.blocksplitWrapper,
args.locations, args)
if None in res:
raise Exception("One of the blocksplit processes failed.")
tempfiles += res
args.locations = []
for f in res:
with open(f) as fp:
for l in fp:
ll = l.strip().split("\t", 3)
if len(ll) < 3:
continue
xchr = ll[0]
start = int(ll[1]) + 1
end = int(ll[2])
args.locations.append("%s:%i-%i" % (xchr, start, end))
else:
pool = None
# count variants before normalisation
if "samples" not in h1 or not h1["samples"]:
raise Exception("Cannot read sample names from truth VCF file")
if args.raw_counts:
counts_truth = Haplo.quantify.run_quantify(
args.vcf1,
None,
None, {"CONF": args.fp_bedfile} if args.fp_bedfile else None,
args.ref,
h1["samples"][0],
locations=args.locations)
else:
counts_truth = None
if "samples" not in h2 or not h2["samples"]:
raise Exception("Cannot read sample names from query VCF file")
if args.raw_counts:
counts_query = Haplo.quantify.run_quantify(
args.vcf2,
None,
None, {"CONF": args.fp_bedfile} if args.fp_bedfile else None,
args.ref,
h2["samples"][0],
locations=args.locations)
else:
counts_query = None
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="hap.py.result.",
suffix=".vcf.gz")
tf.close()
tempfiles.append(tf.name)
output_name = tf.name
if args.engine == "xcmp":
# do xcmp
logging.info("Using xcmp for comparison")
res = runParallel(pool, Haplo.xcmp.xcmpWrapper, args.locations,
args)
tempfiles += [x[0] for x in res if x is not None] # VCFs
tempfiles += [
x[1] for x in res if x is not None and x[1] is not None
] # beds (if any)
if None in res:
raise Exception("One of the xcmp jobs failed.")
if len(res) == 0:
raise Exception(
"Input files/regions do not contain variants (0 haplotype blocks were processed)."
)
# concatenate + index
bedfiles = [
x[1] for x in res if x is not None and x[1] is not None
]
if args.write_bed and bedfiles:
runme = " ".join(["cat"] + bedfiles + [
">",
args.reports_prefix.replace(" ", "\\ ") + ".blocks.bed"
])
logging.info("Concatenating block files: %s..." % runme)
subprocess.check_call(runme, shell=True)
logging.info("Concatenating variants...")
runme_list = [x[0] for x in res if x is not None]
if len(runme_list) == 0:
raise Exception("No outputs to concatenate!")
fo = Tools.BGZipFile(output_name, True)
for i, x in enumerate(runme_list):
f = gzip.GzipFile(x)
for l in f:
if i == 0 or not l[0] == "#":
fo.write(l)
fo.close()
logging.info("Indexing...")
to_run = "tabix -p vcf %s" % output_name.replace(" ", "\\ ")
logging.info("Running '%s'" % to_run)
subprocess.check_call(to_run, shell=True)
elif args.engine == "vcfeval":
tempfiles += Haplo.vcfeval.runVCFEval(args.vcf1, args.vcf2,
output_name, args)
else:
raise Exception("Unknown comparison engine: %s" % args.engine)
if args.write_counts:
json_name = args.reports_prefix + ".counts.json"
else:
tf = tempfile.NamedTemporaryFile(delete=False,
dir=args.scratch_prefix,
prefix="counts.",
suffix=".json")
tf.close()
json_name = tf.name
logging.info("Counting variants...")
counts = Haplo.quantify.run_quantify(
output_name, json_name,
args.reports_prefix + ".vcf.gz" if args.write_vcf else False,
{"CONF": args.fp_bedfile} if args.fp_bedfile else None, args.ref)
df = pandas.DataFrame(counts)
if args.write_counts:
df.to_csv(args.reports_prefix + ".counts.csv")
metrics_output = makeMetricsObject("hap.py.comparison")
if args.write_counts:
metrics_output["metrics"].append(
dataframeToMetricsTable("raw.counts", df))
# calculate precision / recall
count_types = []
if args.raw_counts:
simplified_truth_counts = Haplo.quantify.simplify_counts(
counts_truth, h1["samples"][0:1])
simplified_query_counts = Haplo.quantify.simplify_counts(
counts_query, h2["samples"][0:1])
count_types += simplified_truth_counts.keys()
count_types += simplified_query_counts.keys()
else:
simplified_truth_counts = None
simplified_query_counts = None
simplified_numbers = Haplo.quantify.simplify_counts(counts)
count_types += simplified_numbers.keys()
count_types = sorted(list(set(count_types)))
for vtype in count_types:
if vtype not in simplified_numbers:
simplified_numbers[vtype] = {}
simplified_numbers[vtype]["METRIC.Recall"] = 0
simplified_numbers[vtype]["METRIC.Recall2"] = 0
simplified_numbers[vtype]["METRIC.Precision"] = 0
simplified_numbers[vtype]["METRIC.Frac_NA"] = 0
try:
simplified_numbers[vtype]["METRIC.Recall"] = \
float(simplified_numbers[vtype]["TRUTH.TP"]) / \
float(simplified_numbers[vtype]["TRUTH.TP"] + simplified_numbers[vtype]["TRUTH.FN"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Recall2"] = \
float(simplified_numbers[vtype]["TRUTH.TP"]) / \
float(simplified_numbers[vtype]["TRUTH.TOTAL"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Precision"] = \
float(simplified_numbers[vtype]["QUERY.TP"]) / \
float(simplified_numbers[vtype]["QUERY.TP"] + simplified_numbers[vtype]["QUERY.FP"])
except:
pass
try:
simplified_numbers[vtype]["METRIC.Frac_NA"] = \
float(simplified_numbers[vtype]["QUERY.UNK"]) / \
float(simplified_numbers[vtype]["QUERY.TOTAL"])
except:
pass
try:
simplified_numbers[vtype][
"TRUTH.TOTAL.RAW"] = simplified_truth_counts[vtype][
h1["samples"][0] + ".TOTAL"]
except:
pass
try:
simplified_numbers[vtype][
"QUERY.TOTAL.RAW"] = simplified_query_counts[vtype][
h2["samples"][0] + ".TOTAL"]
except:
pass
pandas.set_option("display.width", 120)
pandas.set_option("display.max_columns", 1000)
df = pandas.DataFrame(simplified_numbers).transpose()
vstring = "hap.py-%s" % Tools.version
vstring += " ".join(sys.argv)
df.loc[vstring] = 0
# for x in df:
# # everything not a metric is a count
# if not x.startswith("METRIC"):
# df[x] = df[x].astype("int64")
df[[
"TRUTH.TOTAL", "QUERY.TOTAL", "METRIC.Recall", "METRIC.Precision",
"METRIC.Frac_NA"
]].to_csv(args.reports_prefix + ".summary.csv")
metrics_output["metrics"].append(
dataframeToMetricsTable(
"summary.metrics", df[[
"TRUTH.TOTAL", "QUERY.TOTAL", "METRIC.Recall",
"METRIC.Precision", "METRIC.Frac_NA"
]]))
if args.write_counts:
df.to_csv(args.reports_prefix + ".extended.csv")
metrics_output["metrics"].append(
dataframeToMetricsTable("all.metrics", df))
essential_numbers = df[[
"TRUTH.TOTAL", "QUERY.TOTAL", "METRIC.Recall", "METRIC.Precision",
"METRIC.Frac_NA"
]]
pandas.set_option('display.max_columns', 500)
pandas.set_option('display.width', 1000)
essential_numbers = essential_numbers[essential_numbers.index.isin(
["Locations.SNP", "Locations.INDEL"])]
logging.info("\n" + str(essential_numbers))
# in default mode, print result summary to stdout
if not args.quiet and not args.verbose:
print "Benchmarking Summary:"
print str(essential_numbers)
if args.roc:
vcf = args.reports_prefix + ".vcf.gz"
res = Haplo.happyroc.roc(vcf, args.roc, args.roc_filter,
args.reports_prefix + ".roc",
args.roc_reversed)
for t in res.iterkeys():
rocdf = pandas.read_table(res[t])
metrics_output["metrics"].append(
dataframeToMetricsTable("roc." + t, rocdf))
with open(args.reports_prefix + ".metrics.json", "w") as fp:
json.dump(metrics_output, fp)
finally:
if args.delete_scratch:
for x in tempfiles:
try:
os.remove(x)
except:
pass
else:
logging.info("Scratch files kept : %s" % (str(tempfiles)))
def partialCredit(vcfname, outputname, reference, locations, threads=1, window=10000, leftshift=True, decompose=True):
""" Partial-credit-process a VCF file according to our args """
pool = getPool(int(threads))
if threads > 1:
logging.info("Partial credit processing uses %i parallel processes." % threads)
if not locations:
h = extractHeadersJSON(vcfname)
if not h["tabix"]["chromosomes"]:
logging.warn("Empty input or not tabix indexed")
if outputname.endswith(".bcf"):
runBcftools("view", "-O", "b", "-o", outputname, vcfname)
runBcftools("index", outputname)
else:
runBcftools("view", "-O", "z", "-o", outputname, vcfname)
runBcftools("index", "-t", outputname)
# just return the same file
return
locations = h["tabix"]["chromosomes"]
elif type(locations) is str or type(locations) is unicode:
locations = locations.split(",")
# use blocksplit to subdivide input
res = runParallel(
pool, blocksplitWrapper, locations, {"vcf": vcfname, "dist": window, "pieces": min(40, threads * 4)}
)
if None in res:
raise Exception("One of the blocksplit processes failed.")
locations = list(itertools.chain.from_iterable(res))
if not len(locations):
logging.warn("Blocksplit returned no blocks. This can happen when " "an input contains no valid variants.")
locations = [""]
else:
locations = [""]
res = []
try:
res = runParallel(
pool,
preprocessWrapper,
itertools.izip(itertools.repeat(vcfname), locations),
{
"reference": reference,
"decompose": decompose,
"leftshift": leftshift,
"bcf": outputname.endswith(".bcf"),
},
)
if None in res:
raise Exception("One of the preprocess jobs failed")
if not res:
raise Exception("No blocks were processed. List of locations: %s" % str(list(locations)))
concatenateParts(outputname, *res)
if outputname.endswith(".vcf.gz"):
runBcftools("index", "-t", outputname)
else: # use bcf
runBcftools("index", outputname)
finally:
for r in res:
try:
os.unlink(r)
except:
pass
try:
os.unlink(r + ".tbi")
except:
pass
try:
os.unlink(r + ".csi")
except:
pass
