def find_core_genome(biosample):
"""
Finds all Genomes with the specified BioSample id that are core genomes
(labelled with CORE)
Args:
biosample: BioSample id of interest
Returns: a list of SPARQL URIs of Genomes that match the BioSample and are
core genomes
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'PREFIX gfvo: <http://www.biointerchange.org/gfvo#>\n'
'SELECT ?Genome \n'
'WHERE {'
'?Genome rdf:type gfvo:Genome .'
'?Genome :has_biosample "%s"^^xsd:string .'
'?Genome :has_sequence ?Sequence .'
'?Sequence :is_from "CORE"^^xsd:string .'
'}' % biosample
)
return [result["Genome"]["value"].split("#", 1)[1] for result in \
results["results"]["bindings"]]
def find_duplicate_biosamples():
"""
Checks to see if a BioSample id is unique or not; if it is not, identify
all Genomes that refer to it
Returns: a list of tuples composed of a BioSample id and a list of SPARQL
URIs for Genomes
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'PREFIX gfvo: <http://www.biointerchange.org/gfvo#>\n'
'SELECT ?BioSample (GROUP_CONCAT( ?Genome ; SEPARATOR = "#") AS \
?Genomes) (COUNT (?Genome) AS ?Elements)\n'
'WHERE { ?Genome rdf:type gfvo:Genome . ?Genome :has_biosample \
?BioSample . '
'MINUS { ?Genome :has_sequence ?Sequence . ?Sequence :is_from \
"WGS"^^xsd:string .}}\n'
'GROUP BY ?BioSample HAVING ( ?Elements > 1)'
)
return (
(
result["BioSample"]["value"],
result["Genomes"]["value"].split("#", )[1::2]
) for result in results["results"]["bindings"])
def check_blank_nodes():
"""
Checks to see if there are any blank nodes present on the database
Returns: a boolean indicating if blank nodes exists or not in the database
"""
results = _sparql_query(
'ASK {?x ?y ?z . FILTER ( isBlank(?x) || isBlank(?z) )}'
)
return results["boolean"]
def find_genome(accession):
"""
Finds the genome instance in Blazegraph. Returns None if nothing is found.
Args:
genome: genome accession number
Returns: the SPARQL URI for the associated genome instance. Returns None if
nothing found.
"""
query = (
'PREFIX : <https://github.com/superphy#>\n'
'SELECT ?s WHERE {?s :has_accession "%s" . }' % accession
)
results = _sparql_query(query)
return results["results"]["bindings"][0]["s"]["value"]
def check_validation(genome):
"""
Checks to see if a particular genome has already had its sequence validated
Args:
genome(str): A genome's accession number
Returns: a boolean indication if the genome has been through validation
(whether validation was true or false)
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX owl: <http://www.w3.org/2002/07/owl#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'ASK { :%s :has_valid_sequence ?o .}' % genome
)
return results["boolean"]
def has_ref_gene(gene_name):
"""
Determines if a particular gene already has a genome its sequence is
referenced from
Args:
gene_name(str): name of the gene
Returns: A boolean, T if is has a reference_gene tag, false if not.
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'ASK {'
':%s :has_copy ?location .'
'?location rdf:type :reference_gene'
'}' % gene_name
)
return results["boolean"]
def find_missing_sequences():
"""
Finds Genome instances in Blazegraph that are missing a sequence and hasn't
failed sequence validation
Returns: list of SPARQL URIs for Genome instances
"""
results = _sparql_query(
'PREFIX : <https://github.com/superphy#>\n'
'PREFIX gfvo: <http://www.biointerchange.org/gfvo#>\n'
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'SELECT ?s ?acc WHERE { ?s rdf:type gfvo:Genome . \
?s :has_accession ?acc . '
'MINUS { ?s :has_valid_sequence ?o }}'
)
return ((result["s"]["value"].rsplit("#", 1)[1], result["acc"]["value"])
for result in results["results"]["bindings"])
def check_named_individual(name):
"""
Checks to see if a given SPARQL URI is an instance of any RDF class encoded
into the database
Args:
name: the SPARQL URI of the instance
(must be from the superphyontology)
Returns: a boolean indicating if the instance exists or not in the database
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX owl: <http://www.w3.org/2002/07/owl#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'ASK { :%s rdf:type owl:NamedIndividual .}' % name
)
return results["boolean"]
def find_source(source):
"""
Finds the correct isolation_from_source instance in Blazegraph given a
term, or returns none if nothing is found
Args:
source: a term used to identify the isolation_from_source
Returns: the SPARQL URI for the associated isolation_from_source or None
"""
results = _sparql_query(
'PREFIX : <https://github.com/superphy#>\n'
'SELECT ?s WHERE {'
'?s ?o "%s"^^xsd:string .'
'?s rdf:type :isolation_from_source'
'}' % source
)
return results["results"]["bindings"][0]["s"]["value"].split("#", 1)[1]
def check_checksum(checksum):
"""
Checks if a particular checksum exists in the database.
As checksums are supposed to be unique to the sequence, if any are found in
the database, the chances of there being a duplicate sequence is high.
Args:
checksum (str): the hash for a sequence
Returns: a boolean indicating if the hash was found in the database
"""
results = _sparql_query(
'PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>\n'
'PREFIX : <https://github.com/superphy#>\n'
'ASK { ?Sequence :has_checksum "%s"^^xsd:string}' % checksum
)
return results["boolean"]
def find_from_host(host):
"""
Finds the correct isolation_from_host instance in Blazegraph given a host
descriptor, or returns none if nothing is found
Args:
host: a term used to identify the host (common or scientifi name,
generally)
Returns: the SPARQL URI for the associated isolation_from_host object or
None
"""
results = _sparql_query(
'PREFIX : <https://github.com/superphy#>\n'
'SELECT ?p WHERE {?s ?o "%s"^^xsd:string . ?s :is_object_of ?p . ?p \
rdf:type :isolation_from_host}' % host
)
return results["results"]["bindings"][0]["p"]["value"].split("#", 1)[1]
