def delete(ctx, variant_file, family_file, family_type, family_id):
"""Delete the variants of a case."""
if not family_file or family_id:
logger.error("Please provide a family file or a case id")
logger.info("Exiting")
ctx.abort()
family = get_family(
family_lines=family_file,
family_type=family_type
)
family_id = family.family_id
affected_individuals = family.affected_individuals
adapter = ctx.obj['adapter']
if variant_file == '-':
logger.info("Start parsing variants from stdin")
variant_stream = get_vcf_handle(fsock=sys.stdin)
else:
logger.info("Start parsing variants from stdin")
variant_stream = get_vcf_handle(infile=variant_file)
start_deleting = datetime.now()
try:
count = delete_variants(adapter, variant_stream, family_id,
affected_individuals)
except CaseError as error:
logger.warning(error.message)
ctx.abort()
logger.info("Nr of variants deleted: {0}".format(count))
logger.info("Time to delete variants: {0}"
.format(datetime.now() - start_deleting))
def get_header(vcf_file_path):
"""Parse the header and return a header object
Args:
vcf_file_path(str): Path to vcf
Returns:
head: A HeaderParser object
"""
logger.info("Parsing header of file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
return head
def variant(self, case_id, variant_id):
"""Return a specific variant.
Args:
case_id (str): Path to vcf file
variant_id (str): A variant id
Returns:
variant (Variant): The variant object for the given id
"""
case_obj = self.case(case_id=case_id)
vcf_file_path = case_obj.variant_source
head = self._get_header(vcf_file_path)
handle = get_vcf_handle(infile=vcf_file_path)
relevant_lines = (line for line in handle if not line.startswith('#'))
for index, variant_line in enumerate(relevant_lines):
index += 1
line_id = get_variant_id(variant_line=variant_line).lstrip('chrCHR')
if line_id == variant_id:
return self._format_variant(
variant_line=variant_line,
index=index,
case_obj=case_obj,
head=head
)
return None
def get_header(vcf_file_path):
"""Parse the header and return a header object
Args:
vcf_file_path(str): Path to vcf
Returns:
head: A HeaderParser object
"""
logger.info("Parsing header of file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
return head
def test_get_vcf_handle_file(self):
"""docstring for test_get_vcf_handle_file"""
file_handle = get_vcf_handle(infile=self.temp_file.name)
result = []
for line in file_handle:
line = line.rstrip()
result.append(line)
assert result == vcf_lines
def test_get_vcf_handle_file(self):
"""docstring for test_get_vcf_handle_file"""
file_handle = get_vcf_handle(infile=self.temp_file.name)
result = []
for line in file_handle:
line = line.rstrip()
result.append(line)
assert result == vcf_lines
def _get_filtered_variants(self, vcf_file_path, filters={}):
"""Check if variants follows the filters
This function will try to make filters faster for the vcf adapter
Args:
vcf_file_path(str): Path to vcf
filters (dict): A dictionary with filters
Yields:
varian_line (str): A vcf variant line
"""
genes = set()
consequences = set()
sv_types = set()
if filters.get('gene_ids'):
genes = set([gene_id.strip() for gene_id in filters['gene_ids']])
if filters.get('consequence'):
consequences = set(filters['consequence'])
if filters.get('sv_types'):
sv_types = set(filters['sv_types'])
logger.info("Get variants from {0}".format(vcf_file_path))
handle = get_vcf_handle(infile=vcf_file_path)
for variant_line in handle:
if not variant_line.startswith('#'):
keep_variant = True
if genes and keep_variant:
keep_variant = False
for gene in genes:
if "{0}".format(gene) in variant_line:
keep_variant = True
break
if consequences and keep_variant:
keep_variant = False
for consequence in consequences:
if consequence in variant_line:
keep_variant = True
break
if sv_types and keep_variant:
keep_variant = False
for sv_type in sv_types:
if sv_type in variant_line:
keep_variant = True
break
if keep_variant:
yield variant_line
def _get_filtered_variants(self, case_obj, filters={}):
"""Check if variants follows the filters
This function will try to make filters faster for the vcf adapter
Args:
case_obj (puzzle.models.Case): A case object
filters (dict): A dictionary with filters
"""
genes = set()
consequences = set()
sv_types = set()
vcf_file_path = case_obj.variant_source
logger.info("Parsing file {0}".format(vcf_file_path))
if filters.get("gene_ids"):
genes = set([gene_id.strip() for gene_id in filters["gene_ids"]])
if filters.get("consequence"):
consequences = set(filters["consequence"])
if filters.get("sv_types"):
sv_types = set(filters["sv_types"])
handle = get_vcf_handle(infile=vcf_file_path)
for variant_line in handle:
if not variant_line.startswith("#"):
keep_variant = True
if genes and keep_variant:
keep_variant = False
for gene in genes:
if "|{0}|".format(gene) in variant_line:
keep_variant = True
break
if consequences and keep_variant:
keep_variant = False
for consequence in consequences:
if consequence in variant_line:
keep_variant = True
break
if sv_types and keep_variant:
keep_variant = False
for sv_type in sv_types:
if sv_type in variant_line:
keep_variant = True
break
if keep_variant:
yield variant_line
def load(ctx, variant_file, family_file, family_type, bulk_insert):
"""Load the variants of a case
The loading is based on if the variant is seen in a ny affected individual
in the family.
"""
if not family_file:
logger.error("Please provide a family file")
ctx.abort()
if variant_file == '-':
logger.info("Parsing variants from stdin")
variant_file = get_vcf_handle(fsock=sys.stdin)
else:
logger.info("Start parsing variants from stdin")
variant_path = os.path.abspath(variant_file)
variant_file = get_vcf_handle(infile=variant_file)
try:
family = get_family(family_lines=family_file, family_type=family_type)
except SyntaxError as error:
logger.warning(error.message)
ctx.abort()
if not family.affected_individuals:
logger.error("No affected individuals could be found in ped file")
ctx.abort()
logger.info("Found affected individuals in ped file: {0}"
.format(', '.join(family.affected_individuals)))
adapter = ctx.obj['adapter']
try:
load_variants(adapter, family.family_id, family.affected_individuals,
variant_file, bulk_insert=bulk_insert,
vcf_path=variant_path)
except CaseError as error:
logger.error(error.message)
ctx.abort()
def _formated_variants(self, raw_variants, case_obj):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
vcf_file_path = case_obj.variant_source
logger.info("Parsing file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith("#"):
if line.startswith("##"):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER"]
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
index = 0
for variant_line in raw_variants:
if not variant_line.startswith("#"):
index += 1
# Create a variant dict:
variant_dict = get_variant_dict(variant_line=variant_line, header_line=header_line)
variant_dict["CHROM"] = variant_dict["CHROM"].lstrip("chrCHR")
# Crreate a info dict:
info_dict = get_info_dict(info_line=variant_dict["INFO"])
# Check if vep annotation:
vep_string = info_dict.get("CSQ")
# Check if snpeff annotation:
snpeff_string = info_dict.get("ANN")
if vep_string:
# Get the vep annotations
vep_info = get_vep_info(vep_string=vep_string, vep_header=vep_header)
elif snpeff_string:
# Get the vep annotations
snpeff_info = get_snpeff_info(snpeff_string=snpeff_string, snpeff_header=snpeff_header)
variant = Variant(**{column: variant_dict.get(column, ".") for column in variant_columns})
logger.debug("Creating a variant object of variant {0}".format(variant.get("variant_id")))
variant["index"] = index
logger.debug("Updating index to: {0}".format(index))
variant["start"] = int(variant_dict["POS"])
if self.variant_type == "sv":
other_chrom = variant["CHROM"]
# If we have a translocation:
if ":" in variant_dict["ALT"] and not "<" in variant_dict["ALT"]:
other_coordinates = variant_dict["ALT"].strip("ACGTN[]").split(":")
other_chrom = other_coordinates[0].lstrip("chrCHR")
other_position = other_coordinates[1]
variant["stop"] = other_position
# Set 'infinity' to length if translocation
variant["sv_len"] = float("inf")
else:
variant["stop"] = int(info_dict.get("END", variant_dict["POS"]))
variant["sv_len"] = variant["stop"] - variant["start"]
variant["stop_chrom"] = other_chrom
else:
variant["stop"] = int(variant_dict["POS"]) + (len(variant_dict["REF"]) - len(variant_dict["ALT"]))
variant["sv_type"] = info_dict.get("SVTYPE")
variant["cytoband_start"] = get_cytoband_coord(chrom=variant["CHROM"], pos=variant["start"])
if variant.get("stop_chrom"):
variant["cytoband_stop"] = get_cytoband_coord(chrom=variant["stop_chrom"], pos=variant["stop"])
# It would be easy to update these keys...
thousand_g = info_dict.get("1000GAF")
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(thousand_g))
variant["thousand_g"] = float(thousand_g)
variant.add_frequency("1000GAF", variant.get("thousand_g"))
# SV specific tag for number of occurances
occurances = info_dict.get("OCC")
if occurances:
logger.debug("Updating occurances to: {0}".format(occurances))
variant["occurances"] = float(occurances)
variant.add_frequency("OCC", occurances)
cadd_score = info_dict.get("CADD")
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(cadd_score))
variant["cadd_score"] = float(cadd_score)
rank_score_entry = info_dict.get("RankScore")
if rank_score_entry:
for family_annotation in rank_score_entry.split(","):
rank_score = family_annotation.split(":")[-1]
logger.debug("Updating rank_score to: {0}".format(rank_score))
variant["rank_score"] = float(rank_score)
genetic_models_entry = info_dict.get("GeneticModels")
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(","):
for genetic_model in family_annotation.split(":")[-1].split("|"):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(rank_score))
variant["genetic_models"] = genetic_models
# Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(variant_dict["FORMAT"].split(":"), variant_dict[sample_id].split(":")))
variant.add_individual(
Genotype(
sample_id=sample_id,
genotype=raw_call.get("GT", "./."),
case_id=individual.case_name,
phenotype=individual.phenotype,
ref_depth=raw_call.get("AD", ",").split(",")[0],
alt_depth=raw_call.get("AD", ",").split(",")[1],
genotype_quality=raw_call.get("GQ", "."),
depth=raw_call.get("DP", "."),
supporting_evidence=raw_call.get("SU", "0"),
pe_support=raw_call.get("PE", "0"),
sr_support=raw_call.get("SR", "0"),
)
)
# Add transcript information:
gmaf = None
if vep_string:
for transcript_info in vep_info:
transcript = self._get_vep_transcripts(transcript_info)
gmaf_raw = transcript_info.get("GMAF")
if gmaf_raw:
gmaf = float(gmaf_raw.split(":")[-1])
variant.add_transcript(transcript)
if gmaf:
variant.add_frequency("GMAF", gmaf)
if not variant.thousand_g:
variant.thousand_g = gmaf
elif snpeff_string:
for transcript_info in snpeff_info:
transcript = self._get_snpeff_transcripts(transcript_info)
variant.add_transcript(transcript)
variant["most_severe_consequence"] = get_most_severe_consequence(variant["transcripts"])
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
yield variant
def get_individuals(vcf=None, case_lines=None, case_type='ped'):
"""Get the individuals from a vcf file, and/or a ped file.
Args:
vcf (str): Path to a vcf
case_lines(Iterable): Ped like lines
case_type(str): Format of ped lines
Returns:
individuals (generator): generator with Individuals
"""
individuals = []
if case_lines:
# read individuals from ped file
family_parser = FamilyParser(case_lines, family_type=case_type)
families = family_parser.families
logger.info("Found families {0}".format(
','.join(list(families.keys()))))
if len(families) != 1:
logger.error("Only one family can be used with vcf adapter")
raise IOError
case_id = list(families.keys())[0]
logger.info("Family used in analysis: {0}".format(case_id))
for ind_id in family_parser.individuals:
ind = family_parser.individuals[ind_id]
logger.info("Found individual {0}".format(ind.individual_id))
individual = Individual(
ind_id=ind.individual_id,
case_id=case_id,
mother=ind.mother,
father=ind.father,
sex=str(ind.sex),
phenotype=str(ind.phenotype),
variant_source=vcf,
)
individuals.append(individual)
elif vcf:
# read individuals from vcf file
case_id = os.path.basename(vcf)
head = HeaderParser()
handle = get_vcf_handle(infile=vcf)
for line in handle:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
for index, ind in enumerate(head.individuals):
# If we only have a vcf file we can not get metadata about the
# individuals
individual = Individual(
ind_id=ind,
case_id=case_id,
variant_source=vcf,
)
individuals.append(individual)
logger.debug("Found individual {0} in {1}".format(
ind, vcf))
return individuals
def test_get_vcf_handle_no_input(self):
"""docstring for test_get_vcf_handle_file"""
with pytest.raises(IOError):
file_handle = get_vcf_handle()
def _formated_variants(self, raw_variants, case_obj):
"""Return variant objects
Args:
raw_variants (Iterable): An iterable with variant lines
case_obj (puzzle.nodels.Case): A case object
"""
vcf_file_path = case_obj.variant_source
logger.info("Parsing file {0}".format(vcf_file_path))
head = HeaderParser()
handle = get_vcf_handle(infile=vcf_file_path)
# Parse the header
for line in handle:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
handle.close()
header_line = head.header
# Get the individual ids for individuals in vcf file
vcf_individuals = set([ind_id for ind_id in head.individuals])
variant_columns = ['CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER']
vep_header = head.vep_columns
snpeff_header = head.snpeff_columns
index = 0
for variant_line in raw_variants:
if not variant_line.startswith('#'):
index += 1
#Create a variant dict:
variant_dict = get_variant_dict(
variant_line = variant_line,
header_line = header_line
)
variant_dict['CHROM'] = variant_dict['CHROM'].lstrip('chrCHR')
#Crreate a info dict:
info_dict = get_info_dict(
info_line = variant_dict['INFO']
)
#Check if vep annotation:
vep_string = info_dict.get('CSQ')
#Check if snpeff annotation:
snpeff_string = info_dict.get('ANN')
if vep_string:
#Get the vep annotations
vep_info = get_vep_info(
vep_string = vep_string,
vep_header = vep_header
)
elif snpeff_string:
#Get the vep annotations
snpeff_info = get_snpeff_info(
snpeff_string = snpeff_string,
snpeff_header = snpeff_header
)
variant = Variant(
**{column: variant_dict.get(column, '.')
for column in variant_columns}
)
logger.debug("Creating a variant object of variant {0}".format(
variant.get('variant_id')))
variant['index'] = index
logger.debug("Updating index to: {0}".format(
index))
variant['start'] = int(variant_dict['POS'])
if self.variant_type == 'sv':
other_chrom = variant['CHROM']
# If we have a translocation:
if ':' in variant_dict['ALT']:
other_coordinates = variant_dict['ALT'].strip('ACGTN[]').split(':')
other_chrom = other_coordinates[0].lstrip('chrCHR')
other_position = other_coordinates[1]
variant['stop'] = other_position
#Set 'infinity' to length if translocation
variant['sv_len'] = float('inf')
else:
variant['stop'] = int(info_dict.get('END', variant_dict['POS']))
variant['sv_len'] = variant['stop'] - variant['start']
variant['stop_chrom'] = other_chrom
else:
variant['stop'] = int(variant_dict['POS']) + \
(len(variant_dict['REF']) - len(variant_dict['ALT']))
variant['sv_type'] = info_dict.get('SVTYPE')
variant['cytoband_start'] = get_cytoband_coord(
chrom=variant['CHROM'],
pos=variant['start'])
if variant.get('stop_chrom'):
variant['cytoband_stop'] = get_cytoband_coord(
chrom=variant['stop_chrom'],
pos=variant['stop'])
# It would be easy to update these keys...
thousand_g = info_dict.get('1000GAF')
if thousand_g:
logger.debug("Updating thousand_g to: {0}".format(
thousand_g))
variant['thousand_g'] = float(thousand_g)
variant.add_frequency('1000GAF', variant.get('thousand_g'))
#SV specific tag for number of occurances
occurances = info_dict.get('OCC')
if occurances:
logger.debug("Updating occurances to: {0}".format(
occurances))
variant['occurances'] = float(occurances)
variant.add_frequency('OCC', occurances)
cadd_score = info_dict.get('CADD')
if cadd_score:
logger.debug("Updating cadd_score to: {0}".format(
cadd_score))
variant['cadd_score'] = float(cadd_score)
rank_score_entry = info_dict.get('RankScore')
if rank_score_entry:
for family_annotation in rank_score_entry.split(','):
rank_score = family_annotation.split(':')[-1]
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['rank_score'] = float(rank_score)
genetic_models_entry = info_dict.get('GeneticModels')
if genetic_models_entry:
genetic_models = []
for family_annotation in genetic_models_entry.split(','):
for genetic_model in family_annotation.split(':')[-1].split('|'):
genetic_models.append(genetic_model)
logger.debug("Updating rank_score to: {0}".format(
rank_score))
variant['genetic_models'] = genetic_models
#Add genotype calls:
for individual in case_obj.individuals:
sample_id = individual.ind_id
if sample_id in vcf_individuals:
raw_call = dict(zip(
variant_dict['FORMAT'].split(':'),
variant_dict[sample_id].split(':'))
)
variant.add_individual(Genotype(
sample_id = sample_id,
genotype = raw_call.get('GT', './.'),
case_id = individual.case_name,
phenotype = individual.phenotype,
ref_depth = raw_call.get('AD', ',').split(',')[0],
alt_depth = raw_call.get('AD', ',').split(',')[1],
genotype_quality = raw_call.get('GQ', '.'),
depth = raw_call.get('DP', '.'),
supporting_evidence = raw_call.get('SU', '0'),
pe_support = raw_call.get('PE', '0'),
sr_support = raw_call.get('SR', '0'),
))
# Add transcript information:
if vep_string:
for transcript in self._get_vep_transcripts(variant, vep_info):
variant.add_transcript(transcript)
elif snpeff_string:
for transcript in self._get_snpeff_transcripts(variant, snpeff_info):
variant.add_transcript(transcript)
variant['most_severe_consequence'] = get_most_severe_consequence(
variant['transcripts']
)
for gene in self._get_genes(variant):
variant.add_gene(gene)
self._add_compounds(variant=variant, info_dict=info_dict)
yield variant
def test_get_vcf_handle_no_input(self):
"""docstring for test_get_vcf_handle_file"""
with pytest.raises(IOError):
file_handle = get_vcf_handle()
