def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
use_gemini = do_db_build(samples) and any(
vcfutils.vcf_has_variants(f) for f in fnames)
name, caller, is_batch = call_info
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "gemini"))
multisample_vcf = get_multisample_vcf(fnames, name, caller, data)
gemini_db = os.path.join(out_dir, "%s-%s.db" % (name, caller))
if not utils.file_exists(gemini_db) and use_gemini:
passonly = all("gemini_allvariants" not in dd.get_tools_on(d)
for d in samples)
gemini_vcf = multiallelic.to_single(multisample_vcf,
data,
passonly=passonly)
ped_file = create_ped_file(samples + extras, gemini_vcf)
# Use original approach for hg19/GRCh37 pending additional testing
if support_gemini_orig(data) and not any(
dd.get_vcfanno(d) for d in samples):
gemini_db = create_gemini_db_orig(gemini_vcf, data, gemini_db,
ped_file)
else:
gemini_db = create_gemini_db(gemini_vcf, data, gemini_db, ped_file)
return [[(name, caller), {
"db": gemini_db if utils.file_exists(gemini_db) else None,
"vcf": multisample_vcf if is_batch else None
}]]
def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "gemini"))
name, caller, is_batch = call_info
gemini_db = os.path.join(out_dir, "%s-%s.db" % (name, caller))
multisample_vcf = get_multisample_vcf(fnames, name, caller, data)
gemini_vcf = multiallelic.to_single(multisample_vcf, data)
use_gemini_quick = (do_db_build(samples) and
any(vcfutils.vcf_has_variants(f) for f in fnames))
if not utils.file_exists(gemini_db) and use_gemini_quick:
use_gemini = do_db_build(samples) and any(vcfutils.vcf_has_variants(f) for f in fnames)
if use_gemini:
ped_file = create_ped_file(samples + extras, gemini_vcf)
gemini_db = create_gemini_db(gemini_vcf, data, gemini_db, ped_file)
return [[(name, caller), {"db": gemini_db if utils.file_exists(gemini_db) else None,
"vcf": multisample_vcf if is_batch else None}]]
def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "gemini"))
name, caller, is_batch = call_info
gemini_db = os.path.join(out_dir, "%s-%s.db" % (name, caller))
multisample_vcf = get_multisample_vcf(fnames, name, caller, data)
gemini_vcf = multiallelic.to_single(multisample_vcf, data)
use_gemini_quick = (do_db_build(samples) and
any(vcfutils.vcf_has_variants(f) for f in fnames))
if not utils.file_exists(gemini_db) and use_gemini_quick:
use_gemini = do_db_build(samples) and any(vcfutils.vcf_has_variants(f) for f in fnames)
if use_gemini:
ped_file = create_ped_file(samples + extras, gemini_vcf)
gemini_db = create_gemini_db(gemini_vcf, data, gemini_db, ped_file)
return [[(name, caller), {"db": gemini_db if utils.file_exists(gemini_db) else None,
"vcf": multisample_vcf if is_batch else None}]]
def prep_gemini_db(fnames, call_info, samples, extras):
"""Prepare a gemini database from VCF inputs prepared with snpEff.
"""
data = samples[0]
use_gemini = do_db_build(samples) and any(vcfutils.vcf_has_variants(f) for f in fnames)
name, caller, is_batch = call_info
out_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "gemini"))
gemini_vcf = get_multisample_vcf(fnames, name, caller, data)
if use_gemini:
passonly = all("gemini_allvariants" not in dd.get_tools_on(d) for d in samples)
gemini_vcf = multiallelic.to_single(gemini_vcf, data, passonly=passonly)
gemini_vcf = _run_vcfanno(gemini_vcf, data, use_gemini)
gemini_db = os.path.join(out_dir, "%s-%s.db" % (name, caller))
if vcfutils.vcf_has_variants(gemini_vcf):
if not utils.file_exists(gemini_db) and use_gemini:
ped_file = create_ped_file(samples + extras, gemini_vcf)
# Use original approach for hg19/GRCh37 pending additional testing
if support_gemini_orig(data) and not any(dd.get_vcfanno(d) for d in samples):
gemini_db = create_gemini_db_orig(gemini_vcf, data, gemini_db, ped_file)
else:
gemini_db = create_gemini_db(gemini_vcf, data, gemini_db, ped_file)
return [[(name, caller), {"db": gemini_db if utils.file_exists(gemini_db) else None,
"vcf": gemini_vcf,
"decomposed": use_gemini}]]