def setupBlazegraph(cls):
"""
Sets up some data for testing methods in this class that queries Blazegraph.
Assumes that Blazegraph is initially empty when testing.
"""
g = Graph()
g.add((n.agn43_AP009048_closed_0, rdf.type, faldo.Region))
g.add((n.agn43_AP009048_closed_0, rdf.type, n.reference_gene))
g.add((n.agn43_AP009048_closed_0, n.is_gene_of, n.AP009048))
g.add((n.agn43_AP009048_closed_0, n.has_sequence, Literal("ACGTTGCA", datatype=XSD.string)))
g.add((n.agn43, n.has_copy, n.agn43_AP009048_closed_0))
g.add((n.agn43_AP009048_closed_0_begin, faldo.position, Literal("2073676", datatype=XSD.string)))
g.add((n.agn43_AP009048_closed_0_end, faldo.position, Literal("2076795", datatype=XSD.string)))
g.add((n.agn43_AP009048_closed_0, faldo.begin, n.agn43_AP009048_closed_0_begin))
g.add((n.agn43_AP009048_closed_0, faldo.end, n.agn43_AP009048_closed_0_end))
g.add((n.agn43, n.has_copy, n.agn43_AP009048_closed_0))
g.add((n.AP009048, n.has_gene, n.agn43_AP009048_closed_0))
g.add((n.ecpC_CP002729_closed_0, rdf.type, faldo.Region))
g.add((n.ecpC_CP002729_closed_0, n.has_sequence, Literal("ACGTTGCA", datatype=XSD.string)))
g.add((n.ecpC, n.has_copy, n.ecpC_CP002729_closed_0))
g.add((n.CP002729, n.has_gene, n.ecpC_CP002729_closed_0))
BlazegraphUploader().upload_data(generate_output(g))
del g
def upload(cls, seqdata, func):
"""Uploads sequence data to Blazegraph based on the inputted function
argument
Args:
seqdata: a SequenceMetadata instance storing sequence-related data
that would otherwise be a data clump:
func: function that handles RDF conversion based on the type of
genome
"""
graph = Graph()
seq_rdf = Sequence(graph, **seqdata.generate_kwargs())
func(seqdata, seq_rdf)
BlazegraphUploader().upload_data(generate_output(graph))
def upload(cls, contigswrapper, func):
"""Uploads contig data to Blazegraph based on inputted function argument
Args:
contigswrapper: ContigsWrapper instance that is a wrapper for
contig metadata
func: function that handles RDF conversion based on the type of
genome
"""
graph = Graph()
for (accession_name, seq) in contigswrapper.contigs:
contig_rdf = Contig(
graph,
**contigswrapper.generate_kwargs(accession_name, seq)
)
func(contigswrapper, contig_rdf)
BlazegraphUploader().upload_data(generate_output(graph))
def create_gene(cls, metadata):
"""
Creates a Gene object to export the data out in the turtle format
with the appropriate RDF tags and
uploads it into Blazegraph.
Args:
metadata(GeneMetadata): An instance that contains metadata
pertaining to an individual gene
"""
graph = Graph()
name = metadata.name
if check_named_individual(name):
print "%s already in Blazegraph." % name
else:
kwargs = metadata.build_kwargs()
Gene(graph, **kwargs).rdf()
BlazegraphUploader().upload_data(generate_output(graph))