def add_reference_resources(data):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
data["reference"] = genome.get_refs(data["genome_build"], aligner,
data["dirs"]["galaxy"])
# back compatible `sam_ref` target
data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base"))
ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"),
utils.get_in(data, ("reference", "fasta", "base")))
data["genome_resources"] = genome.get_resources(data["genome_build"],
ref_loc)
data["reference"]["snpeff"] = effects.get_snpeff_files(data)
alt_genome = utils.get_in(data,
("config", "algorithm", "validate_genome_build"))
if alt_genome:
data["reference"]["alt"] = {
alt_genome:
genome.get_refs(alt_genome, None, data["dirs"]["galaxy"])["fasta"]
}
# Re-enable when we have ability to re-define gemini configuration directory
if False:
if population.do_db_build([data], check_gemini=False, need_bam=False):
data["reference"]["gemini"] = population.get_gemini_files(data)
return data
def add_reference_resources(data, remote_retriever=None):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
if remote_retriever:
data["reference"] = remote_retriever.get_refs(data["genome_build"],
aligner, data["config"])
else:
data["reference"] = genome.get_refs(data["genome_build"], aligner,
data["dirs"]["galaxy"], data)
_check_ref_files(data["reference"], data)
# back compatible `sam_ref` target
data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base"))
ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"),
utils.get_in(data, ("reference", "fasta", "base")))
if remote_retriever:
data = remote_retriever.get_resources(data["genome_build"], ref_loc,
data)
else:
data["genome_resources"] = genome.get_resources(
data["genome_build"], ref_loc, data)
if effects.get_type(
data) == "snpeff" and "snpeff" not in data["reference"]:
data["reference"]["snpeff"] = effects.get_snpeff_files(data)
data = _fill_validation_targets(data)
data = _fill_prioritization_targets(data)
# Re-enable when we have ability to re-define gemini configuration directory
if False:
if population.do_db_build([data], need_bam=False):
data["reference"]["gemini"] = population.get_gemini_files(data)
return data
def add_reference_resources(data, remote_retriever=None):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
if remote_retriever:
data["reference"] = remote_retriever.get_refs(data["genome_build"], aligner, data["config"])
else:
data["reference"] = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"], data)
_check_ref_files(data["reference"], data)
# back compatible `sam_ref` target
data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base"))
ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"),
utils.get_in(data, ("reference", "fasta", "base")))
if remote_retriever:
data = remote_retriever.get_resources(data["genome_build"], ref_loc, data)
else:
data["genome_resources"] = genome.get_resources(data["genome_build"], ref_loc, data)
if effects.get_type(data) == "snpeff" and "snpeff" not in data["reference"]:
data["reference"]["snpeff"] = effects.get_snpeff_files(data)
data = _fill_validation_targets(data)
data = _fill_prioritization_targets(data)
# Re-enable when we have ability to re-define gemini configuration directory
if False:
if population.do_db_build([data], need_bam=False):
data["reference"]["gemini"] = population.get_gemini_files(data)
return data
def _add_reference_resources(data):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
align_ref, sam_ref = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"])
data["align_ref"] = align_ref
data["sam_ref"] = sam_ref
data["genome_resources"] = genome.get_resources(data["genome_build"], sam_ref)
return data
def _add_reference_resources(data):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
align_ref, sam_ref = genome.get_refs(data["genome_build"], aligner,
data["dirs"]["galaxy"])
data["align_ref"] = align_ref
data["sam_ref"] = sam_ref
data["genome_resources"] = genome.get_resources(data["genome_build"],
sam_ref)
return data
def add_reference_resources(data):
"""Add genome reference information to the item to process.
"""
aligner = data["config"]["algorithm"].get("aligner", None)
data["reference"] = genome.get_refs(data["genome_build"], aligner, data["dirs"]["galaxy"])
# back compatible `sam_ref` target
data["sam_ref"] = utils.get_in(data, ("reference", "fasta", "base"))
ref_loc = utils.get_in(data, ("config", "resources", "species", "dir"),
utils.get_in(data, ("reference", "fasta", "base")))
data["genome_resources"] = genome.get_resources(data["genome_build"], ref_loc)
data["reference"]["snpeff"] = effects.get_snpeff_files(data)
alt_genome = utils.get_in(data, ("config", "algorithm", "validate_genome_build"))
if alt_genome:
data["reference"]["alt"] = {alt_genome:
genome.get_refs(alt_genome, None, data["dirs"]["galaxy"])["fasta"]}
# Re-enable when we have ability to re-define gemini configuration directory
if False:
if population.do_db_build([data], check_gemini=False, need_bam=False):
data["reference"]["gemini"] = population.get_gemini_files(data)
return data
