def load_json(json) -> GraphContainer:
"""
Construct graph object from JSON representation
:param json: Dictionary of JSON file contents
"""
graph = GraphContainer()
for node in json["nodes"]:
seqs = node.get("sequences", ())
if "reference" in node:
chrom, start, end = parse_region(node["reference"])
graph.add_refNode(chrom, start, end, seqs, node["name"])
elif "position" in node:
chrom, start, end = parse_region(node["position"])
graph.add_altNode(chrom, start, end, node["sequence"], seqs,
node["name"])
else:
graph.nodes[node["name"]] = node
for edge in json["edges"]:
seqs = edge.get("sequences", ())
graph.add_edge(graph.nodes[edge["from"]], graph.nodes[edge["to"]],
seqs)
graph.name = json["model_name"]
graph.paths = json.get("paths", [])
graph.target_regions = json.get("target_regions", [])
graph.check()
return graph
def convert_vcf(vcf,
ref,
target_regions=None,
ref_node_padding=150,
ref_node_max_length=1000,
allele_graph=False,
simplify=True,
alt_paths=False,
alt_splitting=False):
"""
Convert a single VCF file to a graph dictionary
:param vcf: file name of the VCF file
:param ref: reference FASTA file name
:param target_regions: target region list
:param ref_node_padding: padding / read length
:param ref_node_max_length: maximum length before splitting a reference node
:param allele_graph: add edges between any compatible allele pair, not just haplotypes from input
:param simplify: simplify the graph
:param alt_paths: Add all possible non-reference paths to the graph
:param alt_splitting: also split long alt nodes (e.g. long insertions)
:return: dictionary containing JSON graph
"""
graph = GraphContainer("Graph from %s" % vcf)
indexed_vcf = tempfile.NamedTemporaryFile(delete=False, suffix=".vcf.gz")
try:
indexed_vcf.close()
# noinspection PyUnresolvedReferences
pysam.bcftools.view(vcf, "-o", indexed_vcf.name, "-O", "z", catch_stdout=False) # pylint: disable=no-member
# noinspection PyUnresolvedReferences
pysam.bcftools.index(indexed_vcf.name) # pylint: disable=no-member
regions = map(parse_region, target_regions) if target_regions else [(None,)*3]
for (chrom, start, end) in regions:
if chrom is not None:
logging.info(f"Starting work on region: {chrom}:{start}-{end}")
try:
vcfGraph = VCFGraph.create_from_vcf(
ref, indexed_vcf.name, chrom, start, end, ref_node_padding, allele_graph)
except NoVCFRecordsException:
logging.info(f"Region {chrom}:{start}-{end} has no VCF records, skipping.")
continue
logging.info(f"CONSTRUCTED VCF GRAPH:\n{str(vcfGraph)}")
chromGraph = vcfGraph.get_graph(allele_graph)
if ref_node_max_length:
graphUtils.split_ref_nodes(chromGraph, ref_node_max_length, ref_node_padding)
if alt_splitting:
graphUtils.split_alt_nodes(chromGraph, ref_node_max_length, ref_node_padding)
if simplify:
graphUtils.remove_empty_nodes(chromGraph)
graphUtils.combine_nodes(chromGraph)
# Disable edge label simplification for now. May use node-label short-cut later
# graphUtils.remove_redundant_edge_labels(graph)
chromGraph.check()
graphUtils.add_graph(graph, chromGraph)
finally:
os.remove(indexed_vcf.name)
graph.target_regions = target_regions or graph.get_reference_regions()
graphUtils.add_source_sink(graph)
graphUtils.add_ref_path(graph)
if alt_paths:
graphUtils.add_alt_paths(graph)
graph.check()
return graph.json_dict()