def _snpeff_args_from_config(data):
"""Retrieve snpEff arguments supplied through input configuration.
"""
config = data["config"]
args = ["-hgvs"]
# General supplied arguments
resources = config_utils.get_resources("snpeff", config)
if resources.get("options"):
args += [str(x) for x in resources.get("options", [])]
# cancer specific calling arguments
if vcfutils.get_paired_phenotype(data):
args += ["-cancer"]
effects_transcripts = dd.get_effects_transcripts(data)
if effects_transcripts in set(["canonical_cancer"]):
_, snpeff_base_dir = get_db(data)
canon_list_file = os.path.join(snpeff_base_dir, "transcripts",
"%s.txt" % effects_transcripts)
if not utils.file_exists(canon_list_file):
raise ValueError(
"Cannot find expected file for effects_transcripts: %s" %
canon_list_file)
args += ["-canonList", canon_list_file]
elif effects_transcripts == "canonical" or tz.get_in(
("config", "algorithm", "clinical_reporting"), data):
args += ["-canon"]
return args
def run_vep(in_file, data):
"""Annotate input VCF file with Ensembl variant effect predictor.
"""
if not vcfutils.vcf_has_variants(in_file):
return None
out_file = utils.append_stem(in_file, "-vepeffects")
assert in_file.endswith(".gz") and out_file.endswith(".gz")
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
vep_dir, ensembl_name = prep_vep_cache(data["genome_build"],
tz.get_in(["reference", "fasta", "base"], data))
if vep_dir:
cores = tz.get_in(("config", "algorithm", "num_cores"), data, 1)
fork_args = ["--fork", str(cores)] if cores > 1 else []
vep = config_utils.get_program("vep", data["config"])
is_human = tz.get_in(["genome_resources", "aliases", "human"], data, False)
# HGVS requires a bgzip compressed, faidx indexed input file or is unusable slow
if dd.get_ref_file_compressed(data):
hgvs_compatible = True
config_args = ["--fasta", dd.get_ref_file_compressed(data)]
else:
hgvs_compatible = False
config_args = ["--fasta", dd.get_ref_file(data)]
if is_human:
plugin_fns = {"loftee": _get_loftee, "maxentscan": _get_maxentscan,
"genesplicer": _get_genesplicer, "spliceregion": _get_spliceregion}
plugins = ["loftee"]
if "vep_splicesite_annotations" in dd.get_tools_on(data):
# "genesplicer" too unstable so currently removed
plugins += ["maxentscan", "spliceregion"]
for plugin in plugins:
plugin_args = plugin_fns[plugin](data)
config_args += plugin_args
config_args += ["--sift", "b", "--polyphen", "b"]
if hgvs_compatible:
config_args += ["--hgvs", "--shift_hgvs", "1"]
if (dd.get_effects_transcripts(data).startswith("canonical")
or tz.get_in(("config", "algorithm", "clinical_reporting"), data)):
config_args += ["--pick_allele"]
if ensembl_name.endswith("_merged"):
config_args += ["--merged"]
ensembl_name = ensembl_name.replace("_merged", "")
resources = config_utils.get_resources("vep", data["config"])
extra_args = [str(x) for x in resources.get("options", [])]
cmd = [vep, "--vcf", "-o", "stdout", "-i", in_file] + fork_args + extra_args + \
["--species", ensembl_name,
"--no_stats", "--cache",
"--offline", "--dir", vep_dir,
"--symbol", "--numbers", "--biotype", "--total_length", "--canonical",
"--gene_phenotype", "--ccds", "--uniprot", "--domains", "--regulatory",
"--protein", "--tsl", "--appris", "--af", "--max_af", "--af_1kg", "--af_esp", "--af_gnomad",
"--pubmed", "--variant_class", "--allele_number"] + config_args
perl_exports = utils.get_perl_exports()
# Remove empty fields (';;') which can cause parsing errors downstream
cmd = "%s && %s | sed '/^#/! s/;;/;/g' | bgzip -c > %s" % (perl_exports, " ".join(cmd), tx_out_file)
do.run(cmd, "Ensembl variant effect predictor", data)
if utils.file_exists(out_file):
vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def run_vep(in_file, data):
"""Annotate input VCF file with Ensembl variant effect predictor.
"""
if not vcfutils.vcf_has_variants(in_file):
return None
out_file = utils.append_stem(in_file, "-vepeffects")
assert in_file.endswith(".gz") and out_file.endswith(".gz")
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
vep_dir, ensembl_name = prep_vep_cache(data["genome_build"],
tz.get_in(["reference", "fasta", "base"], data))
if vep_dir:
cores = tz.get_in(("config", "algorithm", "num_cores"), data, 1)
fork_args = ["--fork", str(cores)] if cores > 1 else []
vep = config_utils.get_program("vep", data["config"])
is_human = tz.get_in(["genome_resources", "aliases", "human"], data, False)
# HGVS requires a bgzip compressed, faidx indexed input file or is unusable slow
if dd.get_ref_file_compressed(data):
hgvs_compatible = True
config_args = ["--fasta", dd.get_ref_file_compressed(data)]
else:
hgvs_compatible = False
config_args = ["--fasta", dd.get_ref_file(data)]
if is_human:
plugin_fns = {"loftee": _get_loftee, "maxentscan": _get_maxentscan,
"genesplicer": _get_genesplicer, "spliceregion": _get_spliceregion}
plugins = ["loftee"]
if "vep_splicesite_annotations" in dd.get_tools_on(data):
# "genesplicer" too unstable so currently removed
plugins += ["maxentscan", "spliceregion"]
for plugin in plugins:
plugin_args = plugin_fns[plugin](data)
config_args += plugin_args
config_args += ["--sift", "b", "--polyphen", "b"]
if hgvs_compatible:
config_args += ["--hgvs", "--shift_hgvs", "1"]
if (dd.get_effects_transcripts(data).startswith("canonical")
or tz.get_in(("config", "algorithm", "clinical_reporting"), data)):
config_args += ["--pick_allele"]
if ensembl_name.endswith("_merged"):
config_args += ["--merged"]
ensembl_name = ensembl_name.replace("_merged", "")
resources = config_utils.get_resources("vep", data["config"])
extra_args = [str(x) for x in resources.get("options", [])]
cmd = [vep, "--vcf", "-o", "stdout", "-i", in_file] + fork_args + extra_args + \
["--species", ensembl_name,
"--no_stats", "--cache",
"--offline", "--dir", vep_dir,
"--symbol", "--numbers", "--biotype", "--total_length", "--canonical",
"--gene_phenotype", "--ccds", "--uniprot", "--domains", "--regulatory",
"--protein", "--tsl", "--appris", "--af", "--max_af", "--af_1kg", "--af_esp", "--af_gnomad",
"--pubmed", "--variant_class", "--allele_number"] + config_args
perl_exports = utils.get_perl_exports()
# Remove empty fields (';;') which can cause parsing errors downstream
cmd = "%s && %s | sed '/^#/! s/;;/;/g' | bgzip -c > %s" % (perl_exports, " ".join(cmd), tx_out_file)
do.run(cmd, "Ensembl variant effect predictor", data)
if utils.file_exists(out_file):
return vcfutils.bgzip_and_index(out_file, data["config"])
def run_vep(in_file, data):
"""Annotate input VCF file with Ensembl variant effect predictor.
"""
if not vcfutils.vcf_has_variants(in_file):
return None
out_file = utils.append_stem(in_file, "-vepeffects")
assert in_file.endswith(".gz") and out_file.endswith(".gz")
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
vep_dir, ensembl_name = prep_vep_cache(data["genome_build"],
tz.get_in(["reference", "fasta", "base"], data))
if vep_dir:
cores = tz.get_in(("config", "algorithm", "num_cores"), data, 1)
fork_args = ["--fork", str(cores)] if cores > 1 else []
vep = config_utils.get_program("variant_effect_predictor.pl", data["config"])
is_human = tz.get_in(["genome_resources", "aliases", "human"], data, False)
config_args, config_fields, prediction_fields = [], [], []
if is_human:
plugin_fns = {"dbnsfp": _get_dbnsfp, "loftee": _get_loftee, "dbscsnv": _get_dbscsnv,
"maxentscan": _get_maxentscan, "genesplicer": _get_genesplicer}
plugins = tz.get_in(("config", "resources", "vep", "plugins"), data, ["dbnsfp", "loftee"])
for plugin in plugins:
plugin_args, plugin_fields = plugin_fns[plugin](data)
config_args += plugin_args
config_fields += plugin_fields
config_args += ["--sift", "b", "--polyphen", "b"]
prediction_fields += ["PolyPhen", "SIFT"]
# Use HGVS by default, requires indexing the reference genome
config_args += ["--hgvs", "--shift_hgvs", "1", "--fasta", dd.get_ref_file(data)]
config_fields += ["HGVSc", "HGVSp"]
if (dd.get_effects_transcripts(data).startswith("canonical")
or tz.get_in(("config", "algorithm", "clinical_reporting"), data)):
config_args += ["--pick"]
std_fields = ["Consequence", "Codons", "Amino_acids", "Gene", "SYMBOL", "Feature",
"EXON"] + prediction_fields + ["Protein_position", "BIOTYPE", "CANONICAL", "CCDS"]
resources = config_utils.get_resources("vep", data["config"])
extra_args = [str(x) for x in resources.get("options", [])]
cmd = [vep, "--vcf", "-o", "stdout", "-i", in_file] + fork_args + extra_args + \
["--species", ensembl_name,
"--no_stats",
"--cache", "--offline", "--dir", vep_dir,
"--symbol", "--numbers", "--biotype", "--total_length", "--canonical",
"--gene_phenotype", "--ccds",
"--fields", ",".join(std_fields + config_fields)] + config_args
perl_exports = utils.get_perl_exports()
# Remove empty fields (';;') which can cause parsing errors downstream
cmd = "%s && %s | sed '/^#/! s/;;/;/g' | bgzip -c > %s" % (perl_exports, " ".join(cmd), tx_out_file)
do.run(cmd, "Ensembl variant effect predictor", data)
if utils.file_exists(out_file):
vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
def _snpeff_args_from_config(data):
"""Retrieve snpEff arguments supplied through input configuration.
"""
config = data["config"]
args = ["-hgvs"]
# General supplied arguments
resources = config_utils.get_resources("snpeff", config)
if resources.get("options"):
args += [str(x) for x in resources.get("options", [])]
# cancer specific calling arguments
if vcfutils.get_paired_phenotype(data):
args += ["-cancer"]
effects_transcripts = dd.get_effects_transcripts(data)
if effects_transcripts in set(["canonical_cancer"]):
_, snpeff_base_dir = get_db(data)
canon_list_file = os.path.join(snpeff_base_dir, "transcripts", "%s.txt" % effects_transcripts)
if not utils.file_exists(canon_list_file):
raise ValueError("Cannot find expected file for effects_transcripts: %s" % canon_list_file)
args += ["-canonList", canon_list_file]
elif effects_transcripts == "canonical" or tz.get_in(("config", "algorithm", "clinical_reporting"), data):
args += ["-canon"]
return args
def run_vep(in_file, data):
"""Annotate input VCF file with Ensembl variant effect predictor.
"""
if not vcfutils.vcf_has_variants(in_file):
return None
out_file = utils.append_stem(in_file, "-vepeffects")
assert in_file.endswith(".gz") and out_file.endswith(".gz")
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
vep_dir, ensembl_name = prep_vep_cache(
data["genome_build"],
tz.get_in(["reference", "fasta", "base"], data))
if vep_dir:
cores = tz.get_in(("config", "algorithm", "num_cores"), data,
1)
fork_args = ["--fork", str(cores)] if cores > 1 else []
vep = config_utils.get_program("variant_effect_predictor.pl",
data["config"])
is_human = tz.get_in(["genome_resources", "aliases", "human"],
data, False)
config_args, config_fields, prediction_fields = [], [], []
if is_human:
plugin_fns = {
"dbnsfp": _get_dbnsfp,
"loftee": _get_loftee,
"dbscsnv": _get_dbscsnv,
"maxentscan": _get_maxentscan,
"genesplicer": _get_genesplicer
}
plugins = tz.get_in(
("config", "resources", "vep", "plugins"), data,
["dbnsfp", "loftee"])
for plugin in plugins:
plugin_args, plugin_fields = plugin_fns[plugin](data)
config_args += plugin_args
plugin_fields += plugin_fields
config_args += ["--sift", "b", "--polyphen", "b"]
prediction_fields += ["PolyPhen", "SIFT"]
# Use HGVS by default, requires indexing the reference genome
config_args += [
"--hgvs", "--shift_hgvs", "1", "--fasta",
dd.get_ref_file(data)
]
config_fields += ["HGVSc", "HGVSp"]
if (dd.get_effects_transcripts(data).startswith("canonical")
or tz.get_in(
("config", "algorithm", "clinical_reporting"),
data)):
config_args += ["--pick"]
std_fields = [
"Consequence", "Codons", "Amino_acids", "Gene", "SYMBOL",
"Feature", "EXON"
] + prediction_fields + [
"Protein_position", "BIOTYPE", "CANONICAL", "CCDS"
]
resources = config_utils.get_resources("vep", data["config"])
extra_args = [str(x) for x in resources.get("options", [])]
cmd = [vep, "--vcf", "-o", "stdout", "-i", in_file] + fork_args + extra_args + \
["--species", ensembl_name,
"--no_stats",
"--cache", "--offline", "--dir", vep_dir,
"--symbol", "--numbers", "--biotype", "--total_length", "--canonical",
"--gene_phenotype", "--ccds",
"--fields", ",".join(std_fields + config_fields)] + config_args
perl_exports = utils.get_perl_exports()
# Remove empty fields (';;') which can cause parsing errors downstream
cmd = "%s && %s | sed '/^#/! s/;;/;/g' | bgzip -c > %s" % (
perl_exports, " ".join(cmd), tx_out_file)
do.run(cmd, "Ensembl variant effect predictor", data)
if utils.file_exists(out_file):
vcfutils.bgzip_and_index(out_file, data["config"])
return out_file
