def export(ctx, outfile):
"""Export the variants of a loqus db
The variants are exported to a vcf file
"""
adapter = ctx.obj['adapter']
logger.info("Export the variants from {0}".format(adapter))
nr_cases = 0
existing_chromosomes = set(adapter.get_chromosomes())
ordered_chromosomes = []
for chrom in CHROMOSOME_ORDER:
if chrom in existing_chromosomes:
ordered_chromosomes.append(chrom)
existing_chromosomes.remove(chrom)
for chrom in existing_chromosomes:
ordered_chromosomes.append(chrom)
nr_cases = adapter.cases().count()
logger.info("Found {0} cases in database".format(nr_cases))
head = HeaderParser()
head.add_fileformat("VCFv4.3")
head.add_meta_line("NrCases", nr_cases)
head.add_info("Obs", '1', 'Integer',
"The number of observations for the variant")
head.add_info("Hom", '1', 'Integer', "The number of observed homozygotes")
head.add_info("Hem", '1', 'Integer', "The number of observed hemizygotes")
head.add_version_tracking("loqusdb", __version__,
datetime.now().strftime("%Y-%m-%d %H:%M"))
for chrom in ordered_chromosomes:
length = adapter.get_max_position(chrom)
head.add_contig(contig_id=chrom, length=str(length))
print_headers(head, outfile=outfile)
for chrom in ordered_chromosomes:
for variant in adapter.get_variants(chromosome=chrom):
chrom = variant['chrom']
pos = variant['start']
ref = variant['ref']
alt = variant['alt']
observations = variant['observations']
homozygotes = variant['homozygote']
hemizygotes = variant['hemizygote']
info = "Obs={0}".format(observations)
if homozygotes:
info += ";Hom={0}".format(homozygotes)
if hemizygotes:
info += ";Hem={0}".format(hemizygotes)
variant_line = "{0}\t{1}\t.\t{2}\t{3}\t.\t.\t{4}\n".format(
chrom, pos, ref, alt, info)
print_variant(variant_line=variant_line, outfile=outfile)
def export(ctx, outfile):
"""Export the variants of a loqus db
The variants are exported to a vcf file
"""
adapter = ctx.obj['adapter']
logger.info("Export the variants from {0}".format(adapter))
nr_cases = 0
for nr_cases, case in enumerate(adapter.cases()):
nr_cases += 1
logger.info("Found {0} cases in database".format(nr_cases))
head = HeaderParser()
head.add_fileformat("##fileformat=VCFv4.1")
head.add_meta_line("NrCases", nr_cases)
head.add_info("Obs", '1', 'Integer',
"The number of observations for the variant")
head.add_info("Hom", '1', 'Integer', "The number of observed homozygotes")
head.add_version_tracking("loqusdb", __version__,
datetime.now().strftime("%Y-%m-%d %H:%M"))
logger.debug("Create tempfile to print variants from database")
variants = tempfile.TemporaryFile()
logger.debug("Printing headers")
print_headers(head, outfile=outfile)
try:
for variant in adapter.get_variants():
variant_id = variant['_id'].split('_')
chrom = variant_id[0]
pos = variant_id[1]
ref = variant_id[2]
alt = variant_id[3]
observations = variant['observations']
homozygotes = variant['homozygote']
info = "Obs={0};Hom={1}".format(observations, homozygotes)
variant_line = "{0}\t{1}\t.\t{2}\t{3}\t.\t.\t{4}\n".format(
chrom, pos, ref, alt, info)
variants.write(variant_line)
variants.seek(0)
for line in sort_variants(variants):
print_variant(variant_line=line, outfile=outfile)
finally:
variants.close()
def export(ctx, outfile):
"""Export the variants of a loqus db
The variants are exported to a vcf file
"""
adapter = ctx.obj['adapter']
logger.info("Export the variants from {0}".format(adapter))
nr_cases = 0
for nr_cases, case in enumerate(adapter.cases()):
nr_cases += 1
logger.info("Found {0} cases in database".format(nr_cases))
head = HeaderParser()
head.add_fileformat("##fileformat=VCFv4.1")
head.add_meta_line("NrCases", nr_cases)
head.add_info("Obs", '1', 'Integer', "The number of observations for the variant")
head.add_info("Hom", '1', 'Integer', "The number of observed homozygotes")
head.add_version_tracking("loqusdb", __version__, datetime.now().strftime("%Y-%m-%d %H:%M"))
logger.debug("Create tempfile to print variants from database")
variants = tempfile.TemporaryFile()
logger.debug("Printing headers")
print_headers(head, outfile=outfile)
try:
for variant in adapter.get_variants():
variant_id = variant['_id'].split('_')
chrom = variant_id[0]
pos = variant_id[1]
ref = variant_id[2]
alt = variant_id[3]
observations = variant['observations']
homozygotes = variant['homozygote']
info = "Obs={0};Hom={1}".format(observations, homozygotes)
variant_line = "{0}\t{1}\t.\t{2}\t{3}\t.\t.\t{4}\n".format(
chrom, pos, ref, alt, info)
variants.write(variant_line)
variants.seek(0)
for line in sort_variants(variants):
print_variant(variant_line=line, outfile=outfile)
finally:
variants.close()
def export(ctx, outfile, variant_type):
"""Export the variants of a loqus db
The variants are exported to a vcf file
"""
adapter = ctx.obj['adapter']
version = ctx.obj['version']
LOG.info("Export the variants from {0}".format(adapter))
nr_cases = 0
is_sv = variant_type == 'sv'
existing_chromosomes = set(adapter.get_chromosomes(sv=is_sv))
ordered_chromosomes = []
for chrom in CHROMOSOME_ORDER:
if chrom in existing_chromosomes:
ordered_chromosomes.append(chrom)
existing_chromosomes.remove(chrom)
for chrom in existing_chromosomes:
ordered_chromosomes.append(chrom)
nr_cases = adapter.cases().count()
LOG.info("Found {0} cases in database".format(nr_cases))
head = HeaderParser()
head.add_fileformat("VCFv4.3")
head.add_meta_line("NrCases", nr_cases)
head.add_info("Obs", '1', 'Integer', "The number of observations for the variant")
head.add_info("Hom", '1', 'Integer', "The number of observed homozygotes")
head.add_info("Hem", '1', 'Integer', "The number of observed hemizygotes")
head.add_version_tracking("loqusdb", version, datetime.now().strftime("%Y-%m-%d %H:%M"))
if variant_type == 'sv':
head.add_info("END", '1', 'Integer', "End position of the variant")
head.add_info("SVTYPE", '1', 'String', "Type of structural variant")
head.add_info("SVLEN", '1', 'Integer', "Length of structural variant")
for chrom in ordered_chromosomes:
length = adapter.get_max_position(chrom)
head.add_contig(contig_id=chrom, length=str(length))
print_headers(head, outfile=outfile)
for chrom in ordered_chromosomes:
if variant_type == 'snv':
LOG.info("Collecting all SNV variants")
variants = adapter.get_variants(chromosome=chrom)
else:
LOG.info("Collecting all SV variants")
variants = adapter.get_sv_variants(chromosome=chrom)
LOG.info("{} variants found".format(variants.count()))
for variant in variants:
variant_line = format_variant(variant, variant_type=variant_type)
# chrom = variant['chrom']
# pos = variant['start']
# ref = variant['ref']
# alt = variant['alt']
# observations = variant['observations']
# homozygotes = variant['homozygote']
# hemizygotes = variant['hemizygote']
# info = "Obs={0}".format(observations)
# if homozygotes:
# info += ";Hom={0}".format(homozygotes)
# if hemizygotes:
# info += ";Hem={0}".format(hemizygotes)
# variant_line = "{0}\t{1}\t.\t{2}\t{3}\t.\t.\t{4}\n".format(
# chrom, pos, ref, alt, info)
print_variant(variant_line=variant_line, outfile=outfile)
def cli(variant_file, thousand_g, exac, treshold, outfile, annotate, keyword,
verbose, logfile):
"""
Filter vcf variants based on their frequency.
One can use different sources by addind --keyword multiple times.
Variants and frequency sources should be splitted and normalized(with vt).
"""
loglevel = LEVELS.get(min(verbose,2), "WARNING")
init_log(root_logger, logfile, loglevel)
logger = logging.getLogger(__name__)
#For testing
logger = logging.getLogger("filter_variants.cli.root")
logger.info("Running filter_variants version {0}".format(__version__))
logger.info("Initializing a Header Parser")
head = HeaderParser()
for line in variant_file:
line = line.rstrip()
if line.startswith('#'):
if line.startswith('##'):
head.parse_meta_data(line)
else:
head.parse_header_line(line)
else:
break
if line:
variant_file = itertools.chain([line], variant_file)
if thousand_g:
logger.info("Opening 1000G frequency file with tabix open")
try:
thousand_g_handle = get_tabix_handle(thousand_g)
except OSError as e:
logger.critical(e.message)
logger.info("Exiting")
sys.exit(1)
logger.debug("1000G frequency file opened")
if annotate:
head.add_info(
"1000GAF",
"1",
'Float',
"Frequency in the 1000G database."
)
if exac:
logger.info("Opening ExAC frequency file with tabix open")
try:
exac_handle = get_tabix_handle(exac)
except OSError as e:
logger.critical(e.message)
logger.info("Exiting")
sys.exit(1)
logger.debug("ExAC frequency file opened")
if annotate:
head.add_info(
"ExACAF",
"1",
'Float',
"Frequency in the ExAC database."
)
plugins = []
for key in keyword:
if key not in head.info_dict:
logger.error("{0} is not defined in vcf header.".format(key))
logger.info("Exiting")
sys.exit(1)
plugins.append(Plugin(
name=key,
field='INFO',
data_type='float',
separators=[','],
info_key=key,
record_rule='max',
))
print_headers(head, outfile)
for line in variant_file:
max_freq = 0
line = line.rstrip()
variant_line = line.split('\t')
chrom = variant_line[0].strip('chr')
position = int(variant_line[1])
ref = variant_line[3]
alternative = variant_line[4]
logger.debug("Checking variant {0}".format(
'_'.join([chrom, str(position), ref, alternative])
))
for plugin in plugins:
logger.debug("Getting frequency for {0}".format(
plugin.name))
frequency = plugin.get_value(variant_line=line)
logger.debug("Found frequency {0}".format(
frequency))
if frequency:
if float(frequency) > max_freq:
logger.debug("Updating max freq")
max_freq = float(frequency)
if thousand_g:
logger.debug("Getting thousand g frequency")
frequency = get_frequency(
chrom = chrom,
pos = position,
alt = alternative,
tabix_reader = thousand_g_handle
)
logger.debug("Found frequency {0}".format(
frequency))
if frequency:
if annotate:
line = add_vcf_info(
keyword='1000GAF',
variant_line=line,
annotation=frequency
)
if float(frequency) > max_freq:
logger.debug("Updating max freq")
max_freq = float(frequency)
if exac:
logger.debug("Getting ExAC frequency")
frequency = get_frequency(
chrom = chrom,
pos = position,
alt = alternative,
tabix_reader = exac_handle
)
logger.debug("Found frequency {0}".format(
frequency))
if frequency:
if annotate:
line = add_vcf_info(
keyword='ExACAF',
variant_line=line,
annotation=frequency
)
if float(frequency) > max_freq:
logger.debug("Updating max freq")
max_freq = float(frequency)
if max_freq < treshold:
print_variant(line, outfile)
else:
logger.debug("Frequency {0} is higher than treshold"\
" {1}. Skip printing variant".format(max_freq, treshold))
