def export_causatives(adapter, collaborator):
"""Export causative variants for a collaborator
Args:
adapter(MongoAdapter)
collaborator(str)
Yields:
variant_obj(scout.Models.Variant): Variants marked as causative ordered by position.
"""
# Store the variants in a list for sorting
variants = []
##TODO add check so that same variant is not included more than once
for document_id in adapter.get_causatives(institute_id=collaborator):
variant_obj = adapter.variant(document_id)
chrom = variant_obj['chromosome']
# Convert chromosome to integer for sorting
chrom_int = CHROMOSOME_INTEGERS.get(chrom)
if not chrom_int:
LOG.info("Unknown chromosome %s", chrom)
continue
# Add chromosome and position to prepare for sorting
variants.append((chrom_int, variant_obj['position'], variant_obj))
# Sort varants based on position
variants.sort(key=lambda x: (x[0], x[1]))
for variant in variants:
variant_obj = variant[2]
yield variant_obj
def export_variants(adapter, collaborator, document_id=None, case_id=None):
"""Export causative variants for a collaborator
Args:
adapter(MongoAdapter)
collaborator(str)
document_id(str): Search for a specific variant
case_id(str): Search causative variants for a case
Yields:
variant_obj(scout.Models.Variant): Variants marked as causative ordered by position.
"""
# Store the variants in a list for sorting
variants = []
if document_id:
yield adapter.variant(document_id)
return
variant_ids = adapter.get_causatives(
institute_id=collaborator,
case_id=case_id
)
##TODO add check so that same variant is not included more than once
for document_id in variant_ids:
variant_obj = adapter.variant(document_id)
chrom = variant_obj['chromosome']
# Convert chromosome to integer for sorting
chrom_int = CHROMOSOME_INTEGERS.get(chrom)
if not chrom_int:
LOG.info("Unknown chromosome %s", chrom)
continue
# Add chromosome and position to prepare for sorting
variants.append((chrom_int, variant_obj['position'], variant_obj))
# Sort varants based on position
variants.sort(key=lambda x: (x[0], x[1]))
for variant in variants:
variant_obj = variant[2]
yield variant_obj
def export_variants(adapter, collaborator, document_id=None, case_id=None):
"""Export causative variants for a collaborator
Args:
adapter(MongoAdapter)
collaborator(str)
document_id(str): Search for a specific variant
case_id(str): Search causative variants for a case
Yields:
variant_obj(scout.Models.Variant): Variants marked as causative ordered by position.
"""
# Store the variants in a list for sorting
variants = []
if document_id:
yield adapter.variant(document_id)
return
variant_ids = adapter.get_causatives(institute_id=collaborator,
case_id=case_id)
for doc_id in variant_ids:
variant_obj = adapter.variant(doc_id)
chrom = variant_obj["chromosome"]
# Convert chromosome to integer for sorting
chrom_int = CHROMOSOME_INTEGERS.get(chrom)
if not chrom_int:
LOG.info("Unknown chromosome %s", chrom)
continue
# Add chromosome and position to prepare for sorting
variants.append((chrom_int, variant_obj["position"], variant_obj))
# Sort varants based on position
variants.sort(key=lambda x: (x[0], x[1]))
for variant in variants:
variant_obj = variant[2]
yield variant_obj
def export_panels(adapter, panels, versions=None, build='37'):
"""Export all genes in gene panels
Exports the union of genes in one or several gene panels to a bed like format with coordinates.
Args:
adapter(scout.adapter.MongoAdapter)
panels(iterable(str)): Iterable with panel ids
bed(bool): If lines should be bed formated
"""
if versions and (len(versions) != len(panels)):
raise SyntaxError("If version specify for each panel")
headers = []
build_string = ("##genome_build={}")
headers.append(build_string.format(build))
header_string = (
"##gene_panel={0},version={1},updated_at={2},display_name={3}")
contig_string = ("##contig={0}")
bed_string = ("{0}\t{1}\t{2}\t{3}\t{4}")
# Save all gene ids found in the collection if panels
panel_geneids = set()
# Save all chromosomes found in the collection if panels
chromosomes_found = set()
# Store all hgnc geneobjs
hgnc_geneobjs = []
# Loop over the panels
for i, panel_id in enumerate(panels):
version = None
if versions:
version = versions[i]
panel_obj = adapter.gene_panel(panel_id, version=version)
if not panel_obj:
LOG.warning("Panel {0} version {1} could not be found".format(
panel_id, version))
continue
headers.append(
header_string.format(
panel_obj['panel_name'],
panel_obj['version'],
panel_obj['date'].date(),
panel_obj['display_name'],
))
# Collect the hgnc ids from all genes found
for gene_obj in panel_obj['genes']:
panel_geneids.add(gene_obj['hgnc_id'])
gene_objs = adapter.hgncid_to_gene(build=build)
for hgnc_id in panel_geneids:
hgnc_geneobj = gene_objs.get(hgnc_id)
if hgnc_geneobj is None:
LOG.warn("missing HGNC gene: %s", hgnc_id)
continue
chrom = hgnc_geneobj['chromosome']
start = hgnc_geneobj['start']
chrom_int = CHROMOSOME_INTEGERS.get(chrom)
if not chrom_int:
LOG.warn("Chromosome %s out of scope", chrom)
continue
hgnc_geneobjs.append((chrom_int, start, hgnc_geneobj))
chromosomes_found.add(chrom)
# Sort the genes:
hgnc_geneobjs.sort(key=lambda tup: (tup[0], tup[1]))
for chrom in CHROMOSOMES:
if chrom in chromosomes_found:
headers.append(contig_string.format(chrom))
headers.append("#chromosome\tgene_start\tgene_stop\thgnc_id\thgnc_symbol")
for header in headers:
yield header
for hgnc_gene in hgnc_geneobjs:
gene_obj = hgnc_gene[-1]
gene_line = bed_string.format(gene_obj['chromosome'],
gene_obj['start'], gene_obj['end'],
gene_obj['hgnc_id'],
gene_obj['hgnc_symbol'])
yield gene_line
def export_panels(adapter, panels, versions=None, build='37'):
"""Export all genes in gene panels
Exports the union of genes in one or several gene panels to a bed like format with coordinates.
Args:
adapter(scout.adapter.MongoAdapter)
panels(iterable(str)): Iterable with panel ids
bed(bool): If lines should be bed formated
"""
if versions and (len(versions) != len(panels)):
raise SyntaxError("If version specify for each panel")
headers = []
build_string = ("##genome_build={}")
headers.append(build_string.format(build))
header_string = ("##gene_panel={0},version={1},updated_at={2},display_name={3}")
contig_string = ("##contig={0}")
bed_string = ("{0}\t{1}\t{2}\t{3}\t{4}")
# Save all gene ids found in the collection if panels
panel_geneids = set()
# Save all chromosomes found in the collection if panels
chromosomes_found = set()
# Store all hgnc geneobjs
hgnc_geneobjs = []
# Loop over the panels
for i,panel_id in enumerate(panels):
version = None
if versions:
version = versions[i]
panel_obj = adapter.gene_panel(panel_id, version=version)
if not panel_obj:
LOG.warning("Panel {0} version {1} could not be found".format(panel_id, version))
continue
headers.append(header_string.format(
panel_obj['panel_name'],
panel_obj['version'],
panel_obj['date'].date(),
panel_obj['display_name'],
))
# Collect the hgnc ids from all genes found
for gene_obj in panel_obj['genes']:
panel_geneids.add(gene_obj['hgnc_id'])
gene_objs = adapter.hgncid_to_gene(build=build)
for hgnc_id in panel_geneids:
hgnc_geneobj = gene_objs.get(hgnc_id)
if hgnc_geneobj is None:
LOG.warn("missing HGNC gene: %s", hgnc_id)
continue
chrom = hgnc_geneobj['chromosome']
start = hgnc_geneobj['start']
chrom_int = CHROMOSOME_INTEGERS.get(chrom)
if not chrom_int:
LOG.warn("Chromosome %s out of scope", chrom)
continue
hgnc_geneobjs.append((chrom_int, start, hgnc_geneobj))
chromosomes_found.add(chrom)
# Sort the genes:
hgnc_geneobjs.sort(key=lambda tup: (tup[0], tup[1]))
for chrom in CHROMOSOMES:
if chrom in chromosomes_found:
headers.append(contig_string.format(chrom))
headers.append("#chromosome\tgene_start\tgene_stop\thgnc_id\thgnc_symbol")
for header in headers:
yield header
for hgnc_gene in hgnc_geneobjs:
gene_obj = hgnc_gene[-1]
gene_line = bed_string.format(gene_obj['chromosome'], gene_obj['start'],
gene_obj['end'], gene_obj['hgnc_id'],
gene_obj['hgnc_symbol'])
yield gene_line