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)
