def gene_obj():
"""Get a dictionary with with gene obj information"""
gene = HgncGene(
hgnc_symbol="B3GALT6",
hgnc_id=17978,
ensembl_id="ENSG00000176022",
chrom="1",
start=1232237,
end=1235041,
build="38",
)
return gene
def test_insert_gene(adapter, parsed_gene):
##GIVEN a empty adapter
assert adapter.all_genes().count() == 0
##WHEN inserting a gene
gene_obj = HgncGene(**parsed_gene)
obj_id = adapter.load_hgnc_gene(gene_obj)
##THEN assert that the gene is there
assert adapter.all_genes().count() == 1
##THEN assert that no genes are in the '38' build
assert adapter.all_genes(build='38').count() == 0
def test_insert_many_genes(adapter, parsed_gene):
adapter = adapter
gene_objs = []
##GIVEN a empty adapter
assert adapter.all_genes().count() == 0
##WHEN inserting a bulk of genes
for i in range(300):
parsed_gene['hgnc_id'] = i
gene_objs.append(HgncGene(**parsed_gene))
result = adapter.load_hgnc_bulk(gene_objs)
##THEN assert that the genes are loaded
assert adapter.all_genes().count() == 300
##THEN assert that no genes are in the '38' build
assert adapter.all_genes(build='38').count() == 0
def build_hgnc_gene(gene_info, build="37"):
"""Build a hgnc_gene object
Args:
gene_info(dict): Gene information
Returns:
gene_obj(dict)
{
'_id': ObjectId(),
# This is the hgnc id, required:
'hgnc_id': int,
# The primary symbol, required
'hgnc_symbol': str,
'ensembl_id': str, # required
'build': str, # '37' or '38', defaults to '37', required
'chromosome': str, # required
'start': int, # required
'end': int, # required
'description': str, # Gene description
'aliases': list(), # Gene symbol aliases, includes hgnc_symbol, str
'entrez_id': int,
'omim_id': int,
'pli_score': float,
'primary_transcripts': list(), # List of refseq transcripts (str)
'ucsc_id': str,
'uniprot_ids': list(), # List of str
'vega_id': str,
'transcripts': list(), # List of hgnc_transcript
# Inheritance information
'inheritance_models': list(), # List of model names
'incomplete_penetrance': bool, # Acquired from HPO
# Phenotype information
'phenotypes': list(), # List of dictionaries with phenotype information
}
"""
try:
hgnc_id = int(gene_info["hgnc_id"])
except KeyError as err:
raise KeyError("Gene has to have a hgnc_id")
except ValueError as err:
raise ValueError("hgnc_id has to be integer")
try:
hgnc_symbol = gene_info["hgnc_symbol"]
except KeyError as err:
raise KeyError("Gene has to have a hgnc_symbol")
try:
ensembl_id = gene_info["ensembl_gene_id"]
except KeyError as err:
raise KeyError("Gene has to have a ensembl_id")
try:
chromosome = gene_info["chromosome"]
except KeyError as err:
raise KeyError("Gene has to have a chromosome")
try:
start = int(gene_info["start"])
except KeyError as err:
raise KeyError("Gene has to have a start position")
except TypeError as err:
raise TypeError("Gene start has to be a integer")
try:
end = int(gene_info["end"])
except KeyError as err:
raise KeyError("Gene has to have a end position")
except TypeError as err:
raise TypeError("Gene end has to be a integer")
gene_obj = HgncGene(
hgnc_id=hgnc_id,
hgnc_symbol=hgnc_symbol,
ensembl_id=ensembl_id,
chrom=chromosome,
start=start,
end=end,
build=build,
)
if gene_info.get("description"):
gene_obj["description"] = gene_info["description"]
# LOG.debug("Adding info %s", gene_info['description'])
if gene_info.get("previous_symbols"):
gene_obj["aliases"] = gene_info["previous_symbols"]
if gene_info.get("entrez_id"):
gene_obj["entrez_id"] = int(gene_info["entrez_id"])
if gene_info.get("omim_id"):
gene_obj["omim_id"] = int(gene_info["omim_id"])
if gene_info.get("pli_score"):
gene_obj["pli_score"] = float(gene_info["pli_score"])
if gene_info.get("ref_seq"):
gene_obj["primary_transcripts"] = gene_info["ref_seq"]
if gene_info.get("ucsc_id"):
gene_obj["ucsc_id"] = gene_info["ucsc_id"]
if gene_info.get("uniprot_ids"):
gene_obj["uniprot_ids"] = gene_info["uniprot_ids"]
if gene_info.get("vega_id"):
gene_obj["vega_id"] = gene_info["vega_id"]
if gene_info.get("incomplete_penetrance"):
gene_obj["incomplete_penetrance"] = True
if gene_info.get("inheritance_models"):
gene_obj["inheritance_models"] = gene_info["inheritance_models"]
phenotype_objs = []
for phenotype_info in gene_info.get("phenotypes", []):
phenotype_objs.append(build_phenotype(phenotype_info))
if phenotype_objs:
gene_obj["phenotypes"] = phenotype_objs
for key in list(gene_obj):
if gene_obj[key] is None:
gene_obj.pop(key)
return gene_obj
def build_hgnc_gene(gene_info, build='37'):
"""Build a hgnc_gene object
Args:
gene_info(dict): Gene information
Returns:
gene_obj(dict)
{
'_id': ObjectId(),
# This is the hgnc id, required:
'hgnc_id': int,
# The primary symbol, required
'hgnc_symbol': str,
'ensembl_id': str, # required
'build': str, # '37' or '38', defaults to '37', required
'chromosome': str, # required
'start': int, # required
'end': int, # required
'description': str, # Gene description
'aliases': list(), # Gene symbol aliases, includes hgnc_symbol, str
'entrez_id': int,
'omim_id': int,
'pli_score': float,
'primary_transcripts': list(), # List of refseq transcripts (str)
'ucsc_id': str,
'uniprot_ids': list(), # List of str
'vega_id': str,
'transcripts': list(), # List of hgnc_transcript
# Inheritance information
'inheritance_models': list(), # List of model names
'incomplete_penetrance': bool, # Acquired from HPO
# Phenotype information
'phenotypes': list(), # List of dictionaries with phenotype information
}
"""
try:
hgnc_id = int(gene_info['hgnc_id'])
except KeyError as err:
raise KeyError("Gene has to have a hgnc_id")
except ValueError as err:
raise ValueError("hgnc_id has to be integer")
try:
hgnc_symbol = gene_info['hgnc_symbol']
except KeyError as err:
raise KeyError("Gene has to have a hgnc_symbol")
try:
ensembl_id = gene_info['ensembl_gene_id']
except KeyError as err:
raise KeyError("Gene has to have a ensembl_id")
try:
chromosome = gene_info['chromosome']
except KeyError as err:
raise KeyError("Gene has to have a chromosome")
try:
start = int(gene_info['start'])
except KeyError as err:
raise KeyError("Gene has to have a start position")
except TypeError as err:
raise TypeError("Gene start has to be a integer")
try:
end = int(gene_info['end'])
except KeyError as err:
raise KeyError("Gene has to have a end position")
except TypeError as err:
raise TypeError("Gene end has to be a integer")
gene_obj = HgncGene(
hgnc_id=hgnc_id,
hgnc_symbol=hgnc_symbol,
ensembl_id=ensembl_id,
chrom=chromosome,
start=start,
end=end,
build=build,
)
if gene_info.get('description'):
gene_obj['description'] = gene_info['description']
# LOG.debug("Adding info %s", gene_info['description'])
if gene_info.get('previous_symbols'):
gene_obj['aliases'] = gene_info['previous_symbols']
if gene_info.get('entrez_id'):
gene_obj['entrez_id'] = int(gene_info['entrez_id'])
if gene_info.get('omim_id'):
gene_obj['omim_id'] = int(gene_info['omim_id'])
if gene_info.get('pli_score'):
gene_obj['pli_score'] = float(gene_info['pli_score'])
if gene_info.get('ref_seq'):
gene_obj['primary_transcripts'] = gene_info['ref_seq']
if gene_info.get('ucsc_id'):
gene_obj['ucsc_id'] = gene_info['ucsc_id']
if gene_info.get('uniprot_ids'):
gene_obj['uniprot_ids'] = gene_info['uniprot_ids']
if gene_info.get('vega_id'):
gene_obj['vega_id'] = gene_info['vega_id']
if gene_info.get('incomplete_penetrance'):
gene_obj['incomplete_penetrance'] = True
if gene_info.get('inheritance_models'):
gene_obj['inheritance_models'] = gene_info['inheritance_models']
phenotype_objs = []
for phenotype_info in gene_info.get('phenotypes', []):
phenotype_objs.append(build_phenotype(phenotype_info))
if phenotype_objs:
gene_obj['phenotypes'] = phenotype_objs
for key in list(gene_obj):
if gene_obj[key] is None:
gene_obj.pop(key)
return gene_obj
