def call(ctx, vcf, max_hets, max_het_fraction, minimum_homs, shortest_block,
flag_upd_at_fraction, individual, block_constant, verbose):
"""Call runs of autozygosity. (deprecated: use bcftools roh instead."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
proband_vcf = VCF(vcf)
if len(proband_vcf.samples) > 1:
try:
individual = int(individual)
except TypeError:
logger.warning("Please specify which individual to check.")
ctx.abort()
else:
individual = 0
output_bed_header()
run_rhocall(proband_vcf=proband_vcf,
block_constant=block_constant,
max_hets=max_hets,
max_het_fraction=max_het_fraction,
minimum_homs=minimum_homs,
shortest_block=shortest_block,
flag_UPD_at_fraction=flag_upd_at_fraction,
individual=individual)
def aggregate(roh, quality_threshold, output, verbose):
"""Aggregate runs of autozygosity from rhofile into windowed rho BED file.
Accepts a bcftools roh style TSV-file with CHR,POS,AZ,QUAL."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
logger.info("Running rhocall aggregate {0}".format(__version__))
run_aggregate(roh=roh, quality_threshold=quality_threshold, output=output)
def tally(roh, quality_threshold, flag_upd_at_fraction, output, verbose):
"""Tally runs of autozygosity from rhofile.
Accepts a bcftools roh style TSV-file with CHR,POS,AZ,QUAL."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
logger.info("Running rhocall tally {0}".format(__version__))
run_tally(roh=roh,
quality_threshold=quality_threshold,
flag_upd_at_fraction=flag_upd_at_fraction,
output=output)
def annotate(vcf, roh, bed, v14, quality_threshold, flag_upd_at_fraction,
output, verbose):
"""Markup VCF file using rho-calls. Use BED file to mark all variants in AZ
windows. Alternatively, use a bcftools v>=1.4 file with RG entries to mark
all vars. With the --no-v14 flag, use an older bcftools v<=1.2 style roh TSV
to mark only selected AZ variants. Roh is broken in bcftools v1.3
- do not use."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
proband_vcf = VCF(vcf)
# add this command to VCF header
## This is for logging the command line string ##
frame = inspect.currentframe()
args, _, _, values = inspect.getargvalues(frame)
argument_list = [
i + '=' + str(values[i]) for i in values
if values[i] and i not in ['frame']
]
logger.info("Running rhocall annotate {0}".format(__version__))
logger.debug("Arguments: {0}".format(', '.join(argument_list)))
## add additional tags to VCF header
proband_vcf.add_to_header('##rhocall_version={0}'.format(__version__))
proband_vcf.add_to_header("##rhocall_arguments={0}".format(
', '.join(argument_list)))
if roh and not bed and not v14:
run_annotate_var(proband_vcf=proband_vcf,
roh=roh,
quality_threshold=quality_threshold,
flag_upd_at_fraction=flag_upd_at_fraction,
output=output)
elif roh and v14 and not bed:
run_annotate_rg(proband_vcf=proband_vcf,
bcfroh=roh,
quality_threshold=quality_threshold,
flag_upd_at_fraction=flag_upd_at_fraction,
output=output)
elif bed and not roh:
run_annotate(proband_vcf=proband_vcf,
bed=bed,
quality_threshold=quality_threshold,
flag_upd_at_fraction=flag_upd_at_fraction,
output=output)
else:
click.echo("""Cannot use both BED and ROH at once. Please apply
them sequentially instead.""")
def viz(vcf, out_dir, wig, pointsize, rho, minsnv, maxsnv, minaf, maxaf, aftag,
minqual, mnv, window, rsid, filter, verbose):
"""Plot binned zygosity and RHO-regions."""
loglevel = LEVELS.get(min(verbose, 3))
configure_stream(level=loglevel)
if not os.access(out_dir, os.F_OK):
os.mkdir(out_dir)
binned_zygosity = generate_bins(vcf, window, filter, mnv, minqual, rsid,
minaf, aftag, maxaf, minsnv)
roh = extract_roh(rho)
if wig:
out_file_basename = out_dir + "/output"
generate_wig(binned_zygosity, roh, window, out_file_basename)
else:
generate_plots(binned_zygosity, roh, window, pointsize, out_dir)