def create_contig_info(dict_edges, input_dirpath, output_dirpath, contig_edges,
edges_by_component, edges_by_repeat_component,
edges_by_ref_component, assembler):
contig_info = None
if is_canu(assembler):
contig_info = parse_canu_contigs_info(input_dirpath)
elif is_flye(assembler):
contig_info = parse_flye_contigs_info(input_dirpath)
elif is_spades(assembler):
contig_info = parse_spades_contigs_info(input_dirpath, contig_edges)
if not contig_info:
with open(join(output_dirpath, 'contig_info.json'), 'a') as handle:
handle.write("contigInfo=" + json.dumps([]) + ";\n")
with open(join(output_dirpath, 'edges_base_info.json'), 'w') as handle:
handle.write("edgeInfo=" + json.dumps([]) + ";")
handle.write("medianCov=" +
json.dumps(calculate_median_cov(dict_edges)) + ";\n")
return
edge_contigs = defaultdict(set)
for contig, data in contig_info.items():
subgraph = None
repeat_subgraph = None
ref_subgraph = None
edges = data['edges']
for edge_name in set(edges):
edge_id = get_edge_agv_id(edge_name)
if edge_id in dict_edges:
edge_contigs[edge_id].add(contig)
match_edge_id = get_match_edge_id(edge_id)
if match_edge_id in dict_edges:
edge_contigs[match_edge_id].add(contig)
if not subgraph and edge_id in edges_by_component:
data['g'] = edges_by_component[edge_id]
if not repeat_subgraph and edge_id in edges_by_repeat_component:
data['rep_g'] = edges_by_repeat_component[edge_id]
if not ref_subgraph and edge_id in edges_by_ref_component:
data['ref_g'] = edges_by_ref_component[edge_id]
data['num_edges'] = str(len(edges))
contig_info[contig] = data
for edge_id in edge_contigs:
edge_contigs[edge_id] = list(edge_contigs[edge_id])
with open(join(output_dirpath, 'contig_info.json'), 'a') as handle:
handle.write("contigInfo=" + json.dumps(contig_info) + ";\n")
with open(join(output_dirpath, 'edges_base_info.json'), 'w') as handle:
handle.write("edgeInfo=" + json.dumps(edge_contigs) + ";")
handle.write("medianCov=" +
json.dumps(calculate_median_cov(dict_edges)) + ";\n")
return
def parse_alignments(alignments_fpath, json_output_dirpath):
gaps_info = defaultdict(list)
chrom_alignments = defaultdict(list)
ms_info = defaultdict(list)
aligns_by_chroms = defaultdict(list)
# S1 E1 S2 E2 Reference Contig IDY Ambiguous Best_group
with open(alignments_fpath) as f:
for i, line in enumerate(f):
if i == 0:
continue
fs = line.split('\t')
if len(fs) > 5:
start, end, start2, end2, chrom, edge_id = fs[:6]
start, end = int(start), int(end)
if int(start2) > int(end2):
edge_id = get_match_edge_id(edge_id)
chrom_alignments[chrom].append((start, end, edge_id))
elif line.startswith("relocation") or line.startswith(
"transloc") or line.startswith("invers"):
ms_info[(chrom, start, end)].append(line.strip())
for chrom, alignments in chrom_alignments.items():
alignments.sort(key=lambda x: (x[0], x[1]))
prev_end = 0
for start, end, edge_id in alignments:
if start - prev_end > GAP_THRESHOLD:
gaps_info[chrom].append((prev_end, start - 1))
prev_end = max(prev_end, end)
align = {
's': start,
'e': end,
'edge': edge_id,
'ms': ';'.join(ms_info[(chrom, start, end)])
}
aligns_by_chroms[chrom].append(align)
with open(join(json_output_dirpath, 'reference.json'), 'w') as handle:
handle.write("chromGaps=" + json.dumps(gaps_info) + ";\n")
handle.write("chromAligns=" + json.dumps(aligns_by_chroms) + ";\n")
def parse_gfa(gfa_fpath, min_edge_len, input_dirpath=None, assembler=None):
dict_edges = dict()
predecessors = defaultdict(list)
successors = defaultdict(list)
g = nx.DiGraph()
print("Parsing " + gfa_fpath + "...")
# gfa = gfapy.Gfa.from_file(gfa_fpath, vlevel = 0)
links = []
edge_overlaps = defaultdict(dict)
with open(gfa_fpath) as f:
for line in f:
record_type = line[0]
if record_type == 'S':
fs = line.split()
name, seq_len = fs[1], len(fs[2])
if fs[2] == '*':
seq_len = None
add_fields = fs[3:] if len(fs) > 3 else []
add_info = dict((f.split(':')[0].lower(), f.split(':')[-1]) for f in add_fields)
cov = 1
if "dp" in add_info:
cov = float(add_info["dp"]) ## coverage depth
elif "kc" in add_info:
cov = max(1, int(add_info["kc"]) / seq_len) ## k-mer count / edge length
if "ln" in add_info:
seq_len = int(add_info["ln"]) ## sequence length
if seq_len and seq_len >= min_edge_len:
edge_id = get_edge_agv_id(get_edge_num(name))
edge = Edge(edge_id, get_edge_num(name), seq_len, cov, element_id=edge_id)
dict_edges[edge_id] = edge
for overlapped_edge, overlap in edge_overlaps[edge_id].items():
dict_edges[edge_id].overlaps.append((edge_id_to_name(overlapped_edge), overlapped_edge, overlap))
rc_edge_id = get_edge_agv_id(-get_edge_num(name))
rc_edge = Edge(rc_edge_id, -get_edge_num(name), seq_len, cov, element_id=rc_edge_id)
dict_edges[rc_edge_id] = rc_edge
for overlapped_edge, overlap in edge_overlaps[rc_edge_id].items():
dict_edges[edge_id].overlaps.append((edge_id_to_name(overlapped_edge), overlapped_edge, overlap))
if record_type != 'L' and record_type != 'E':
continue
if record_type == 'L':
_, from_name, from_orient, to_name, to_orient = line.split()[:5]
else:
# E * 2+ 65397+ 21 68$ 0 47 47M
from_name, to_name = line.split()[2], line.split()[3]
from_orient, to_orient = from_name[-1], to_name[-1]
from_name, to_name = from_name[:-1], to_name[:-1]
edge1 = get_edge_agv_id(get_edge_num(from_name))
edge2 = get_edge_agv_id(get_edge_num(to_name))
if from_orient == '-': edge1 = get_match_edge_id(edge1)
if to_orient == '-': edge2 = get_match_edge_id(edge2)
overlap = 0
overlap_operations = re.split('(\d+)', line.split()[-1].strip())
for i in range(0, len(overlap_operations) - 1, 1):
if not overlap_operations[i]:
continue
if overlap_operations[i+1] == 'M' or overlap_operations[i+1] == 'I':
overlap += int(overlap_operations[i])
links.append((from_name, from_orient, to_name, to_orient, overlap))
if overlap:
edge_overlaps[edge1][edge2] = overlap
edge_overlaps[edge2][edge1] = overlap
### gfa retains only canonical links
for link in links:
from_name, from_orient, to_name, to_orient, overlap = link
edge1 = get_edge_agv_id(get_edge_num(from_name))
edge2 = get_edge_agv_id(get_edge_num(to_name))
if from_orient == '-': edge1 = get_match_edge_id(edge1)
if to_orient == '-': edge2 = get_match_edge_id(edge2)
if edge1 != edge2:
predecessors[edge2].append(edge1)
successors[edge1].append(edge2)
g.add_edge(edge1, edge2)
if is_spades(assembler) or is_abyss(assembler):
edge1, edge2 = get_match_edge_id(edge2), get_match_edge_id(edge1)
if edge1 != edge2:
predecessors[edge2].append(edge1)
successors[edge1].append(edge2)
g.add_edge(edge1, edge2)
if assembler == "canu" and input_dirpath:
dict_edges = parse_canu_unitigs_info(input_dirpath, dict_edges)
dict_edges = construct_graph(dict_edges, predecessors, successors)
print("Finish parsing.")
return dict_edges
def process_graph(g, undirected_g, dict_edges, edges_by_nodes, two_way_edges, output_dirpath, suffix, assembler,
base_graph=None, contig_edges=None, chrom_names=None, edge_by_chrom=None, mapping_info=None):
last_idx = 0
parts_info = dict()
graph = []
modified_dict_edges = dict()
loop_edges = defaultdict(set)
hanging_nodes = []
connected_nodes = []
enters = []
exits = []
base_graph = base_graph or g
chrom_list = []
contig_list = []
complex_component = False
if suffix == "ref":
if chrom_names:
## create graph for reference-based mode
for chrom in list(natural_sort(chrom_names)):
edges = edge_by_chrom[chrom] # use only edges mapped to the chromosome
graph_component = nx.DiGraph()
for edge_id in set(edges):
graph_component.add_edge(dict_edges[edge_id].start, dict_edges[edge_id].end)
viewer_data, last_idx, sub_complex_component = \
split_graph(graph_component, g, undirected_g, dict_edges, modified_dict_edges, loop_edges, edges_by_nodes,
two_way_edges, last_idx, parts_info, mapping_info=mapping_info, chrom=chrom)
parts_info = viewer_data.parts_info
graph.extend(viewer_data.g)
for i in range(len(viewer_data.g)):
chrom_list.append(chrom)
complex_component = complex_component or sub_complex_component
with open(join(output_dirpath, 'reference.json'), 'a') as handle:
handle.write("chromosomes=" + json.dumps(chrom_list) + ";\n")
elif contig_edges and suffix == "contig":
## create graph for contig-focused mode
for contig, edges in contig_edges.items():
graph_component = nx.DiGraph()
edge_ids = set()
for edge in edges:
_, _, edge_id = edge
edge_ids.add(edge_id)
edge_ids.add(get_match_edge_id(edge_id))
filtered_edge_ids = set()
for edge_id in edge_ids:
if edge_id in dict_edges:
graph_component.add_edge(dict_edges[edge_id].start, dict_edges[edge_id].end)
filtered_edge_ids.add(edge_id)
viewer_data, last_idx, sub_complex_component = \
split_graph(graph_component, g, undirected_g, dict_edges, modified_dict_edges, loop_edges, edges_by_nodes,
two_way_edges, last_idx, parts_info, contig_edges=filtered_edge_ids)
parts_info = viewer_data.parts_info
for i in range(len(viewer_data.g)):
contig_list.append(contig)
graph.extend(viewer_data.g)
with open(join(output_dirpath, 'contig_info.json'), 'w') as handle:
handle.write("contigs=" + json.dumps(contig_list) + ";\n")
elif suffix == "repeat" or suffix == "def":
fake_edges = []
if is_flye(assembler):
## add fake edges to keep forward and reverse complement components of an edge together
for edge_id, edge in dict_edges.items():
if edge_id.startswith("rc"): continue
if suffix == "repeat" and not edge.repetitive: continue
match_edge_id = get_match_edge_id(edge_id)
if match_edge_id not in dict_edges: continue
match_edge_nodes = [dict_edges[match_edge_id].start, dict_edges[match_edge_id].end]
if not any([e in undirected_g.neighbors(edge.start) for e in match_edge_nodes]) and not \
any([e in undirected_g.neighbors(edge.end) for e in match_edge_nodes]):
g.add_edge(edge.end, dict_edges[match_edge_id].start)
g.add_edge(edge.start, dict_edges[match_edge_id].end)
fake_edges.append((edge.start, dict_edges[match_edge_id].end))
fake_edges.append((edge.end, dict_edges[match_edge_id].start))
# split graph into connected components
connected_components = list(nx.weakly_connected_component_subgraphs(g))
if fake_edges:
g.remove_edges_from(fake_edges)
for i, graph_component in enumerate(connected_components):
viewer_data, last_idx, sub_complex_component = \
split_graph(graph_component, base_graph, undirected_g, dict_edges, modified_dict_edges, loop_edges, edges_by_nodes,
two_way_edges, last_idx, parts_info,
fake_edges=fake_edges, find_hanging_nodes=suffix == "def", is_repeat_graph=suffix == "repeat")
parts_info = viewer_data.parts_info
graph.extend(viewer_data.g)
hanging_nodes.extend(viewer_data.hanging_nodes)
connected_nodes.extend(viewer_data.connected_nodes)
enters.extend(viewer_data.enters)
exits.extend(viewer_data.exits)
edges_by_component = save_graph(graph, hanging_nodes, connected_nodes, enters, exits, dict_edges, modified_dict_edges,
loop_edges, parts_info, output_dirpath, suffix,
complex_component=complex_component,
mapping_info=mapping_info, chrom_list=chrom_list, contig_list=contig_list)
return edges_by_component
def parse_mapping_info(mapping_fpath, json_output_dir, dict_edges):
# assign edges to chromosomes and color edges to corresponding colors
mapping_info = defaultdict(set)
edge_mappings = defaultdict(lambda: defaultdict(list))
edge_lengths = dict()
chrom_lengths = dict()
with open(mapping_fpath) as f:
for line in f:
# contig_1 257261 14 160143 - chr13 924431 196490 356991 147365 161095 60 tp:A:P cm:i:14049 s1:i:147260 s2:i:4375 dv:f:0.0066
fs = line.split()
edge_id = get_edge_agv_id(get_edge_num(fs[0]))
start, end = int(fs[2]), int(fs[3])
edge_lengths[edge_id] = int(fs[1])
chrom, chrom_len = fs[5], int(fs[6])
ref_start, ref_end = int(fs[7]), int(fs[8])
chrom_lengths[chrom] = chrom_len
edge_mappings[edge_id][chrom].append(
(start, end, ref_start, ref_end))
chroms_by_edge = defaultdict(set)
edge_by_chrom = defaultdict(set)
chrom_names = set()
best_aligns = defaultdict(defaultdict)
for edge_id in edge_mappings:
# assign an edge to a chromosome if more than 90% of edge aligned to the chromosome
len_threshold = 0.9 * edge_lengths[edge_id]
gap_threshold = min(5000, 0.05 * edge_lengths[edge_id])
for chrom, mappings in edge_mappings[edge_id].items():
mappings.sort(key=lambda x: (x[0], -x[1]), reverse=False)
for chrom, mappings in edge_mappings[edge_id].items():
aligns = []
covered_len = 0
last_pos = 0
last_ref_pos = 0
align_s, align_e = 0, 0
# calculate covered length (do not count overlaps)
for (start, end, ref_start, ref_end) in mappings:
start = max(start, last_pos)
covered_len += max(0, end - start + 1)
last_pos = max(last_pos, end + 1)
if covered_len >= len_threshold:
chroms_by_edge[edge_id].add(chrom)
chrom_names.add(chrom)
edge_by_chrom[chrom].add(edge_id)
mappings.sort(key=lambda x: (x[2], -x[3]), reverse=False)
for (start, end, ref_start, ref_end) in mappings:
ref_start = max(ref_start, last_ref_pos)
last_ref_pos = max(last_ref_pos, ref_end + 1)
if not align_s:
align_s = ref_start
if align_e and ref_start - align_e >= gap_threshold:
if align_e - align_s >= 500: # break alignments if gap longer than 500 bp
aligns.append((chrom, align_s, align_e))
align_s = ref_start
align_e = ref_end - 1
if align_e and align_e - align_s >= 500:
aligns.append((chrom, align_s, align_e))
aligns.sort(reverse=True, key=lambda x: x[2] - x[1])
edge_alignment = chrom + ":"
if aligns:
best_aligns[edge_id][chrom] = aligns[0][1]
for align in aligns[:
3]: # store top 3 alignments for each edge
edge_alignment += " %s-%s," % (format_pos(
align[1]), format_pos(align[2]))
dict_edges[edge_id].aligns[chrom] = edge_alignment[:-1]
if get_match_edge_id(edge_id) in dict_edges:
dict_edges[get_match_edge_id(
edge_id)].aligns[chrom] = edge_alignment[:-1]
chrom_len_dict = OrderedDict(
(chrom, chrom_lengths[chrom])
for i, chrom in enumerate(list(natural_sort(chrom_names))))
non_alt_chroms = [
c for c in chrom_names
if 'alt' not in c and 'random' not in c and 'chrUn' not in c
]
chrom_order = OrderedDict(
(chrom, i)
for i, chrom in enumerate(list(natural_sort(non_alt_chroms))))
color_list = [
'#e6194b', '#3cb44b', '#ffe119', '#1792d4', '#f58231', '#911eb4',
'#46f0f0', '#f032e6', '#d2f53c', '#fabebe', '#00dbb1', '#dba2ff',
'#aa6e28', '#83360e', '#800000', '#003bff', '#808000', '#8d73d4',
'#000080', '#806680', '#51205a', '#558859', '#d1a187', '#87a1d1',
'#87a1d1', '#afd187'
]
edge_chroms = defaultdict(set)
for edge_id, chroms in chroms_by_edge.items():
match_edge_id = edge_id.replace(
'rc', 'e') if edge_id.startswith('rc') else edge_id.replace(
'e', 'rc')
for chrom in chroms:
edge_chroms[edge_id].add(chrom)
edge_chroms[match_edge_id].add(chrom)
if match_edge_id in dict_edges:
edge_by_chrom[chrom].add(match_edge_id)
is_single_chrom = len(chrom_order.keys()) == 1
for edge_id, chroms in edge_chroms.items():
if edge_id not in dict_edges:
continue
mapping_info[edge_id] = list(chroms)
colors = set()
for chrom in chroms:
if chrom in chrom_order:
if is_single_chrom: # color an edge according to its position in reference
pos = best_aligns[edge_id][chrom] if best_aligns[edge_id] else \
best_aligns[get_match_edge_id(edge_id)][chrom]
color = get_rainbow_color(pos, chrom_len_dict[chrom])
else:
color = color_list[chrom_order[chrom] % len(color_list)]
else:
color = '#808080'
colors.add(color)
if len(colors) <= 5:
dict_edges[edge_id].chrom = ':'.join(list(colors))
else:
dict_edges[edge_id].chrom = 'white:red:black:red:black:white'
with open(join(json_output_dir, "reference.json"), 'a') as handle:
handle.write("chrom_lengths=" + json.dumps(chrom_len_dict) + ";\n")
handle.write("edgeMappingInfo=" + json.dumps(mapping_info) + ";\n")
return mapping_info, non_alt_chroms, edge_by_chrom