def fastg_to_gfa(input_fpath, output_dirpath, assembler_name):
k8_exec = join(TOOLS_DIR, "k8-darwin") if is_osx() else join(
TOOLS_DIR, "k8-linux")
gfatools_exec = join(TOOLS_DIR, "gfatools.js")
if gfatools_exec and k8_exec:
output_fpath = join(output_dirpath,
basename(input_fpath).replace("fastg", "gfa"))
cmd = None
if is_abyss(assembler_name):
cmd = "abyss2gfa"
elif is_spades(assembler_name):
cmd = "spades2gfa"
elif is_sga(assembler_name):
cmd = "sga2gfa"
elif is_soap(assembler_name):
cmd = "soap2gfa"
elif is_velvet(assembler_name):
cmd = "velvet2gfa"
if not cmd:
sys.exit(
"FASTG files produced by " + assembler_name +
" are not supported. Supported assemblers: " + ' '.join([
ABYSS_NAME, SGA_NAME, SOAP_NAME, SPADES_NAME, VELVET_NAME
]) + " or use files in GFA format.")
cmdline = [k8_exec, gfatools_exec, cmd, input_fpath]
subprocess.call(cmdline,
stdout=output_fpath,
stderr=open("/dev/null", "w"))
if not is_empty_file(output_fpath):
return output_fpath
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_assembler_output(assembler_name, input_dirpath, input_fpath,
output_dirpath, input_fasta_fpath, min_edge_len):
edges_fpath = None
if not is_empty_file(input_fpath):
contig_edges = []
if input_fpath.endswith("fastg"):
input_fpath = fastg_to_gfa(input_fpath, output_dirpath,
assembler_name)
if not input_fpath:
sys.exit("ERROR! Failed parsing " + input_fpath + " file.")
if input_fpath.endswith("gfa") or input_fpath.endswith("gfa2"):
dict_edges = parse_gfa(input_fpath, min_edge_len)
edges_fpath = get_edges_from_gfa(input_fpath, output_dirpath,
min_edge_len)
elif input_fpath.endswith("dot") or input_fpath.endswith("gv"):
edges_fpath = format_edges_file(input_fasta_fpath, output_dirpath)
dict_edges = dict()
if is_abyss(assembler_name):
dict_edges = parse_abyss_dot(input_fpath, min_edge_len)
if not dict_edges:
try:
dict_edges = parse_flye_dot(input_fpath, min_edge_len)
except Exception as e:
sys.exit(
"ERROR! Failed parsing " + input_fpath + " file.\n"
"During parsing the following error has occured: " +
str(e) +
"\nPlease make sure that you correctly specified the assembler name using -a option. "
"DOT files produced by different assemblers can have very different formats.\n"
"Examples of input data can be found here https://github.com/almiheenko/AGB/tree/master/test_data"
)
else:
if is_canu(assembler_name):
dict_edges, contig_edges, edges_fpath = parse_canu_output(
input_dirpath, output_dirpath, min_edge_len)
elif is_flye(assembler_name):
dict_edges, contig_edges, edges_fpath = parse_flye_output(
input_dirpath, output_dirpath, min_edge_len)
elif is_spades(assembler_name):
dict_edges, contig_edges, edges_fpath = parse_spades_output(
input_dirpath, output_dirpath, min_edge_len)
else:
sys.exit(
"Output folder of %s assembler can not be parsed! Supported assemblers: %s. "
"More assemblers will be added in the next release.\n"
"To visualize the assembly graph produced by this assembler, "
"you should manually specify the assembly graph file in GFA/FASTG/GraphViz formats using --graph option "
"and (optionally) file with edge sequences using --fasta option"
% (assembler_name, ', '.join(SUPPORTED_ASSEMBLERS)))
for edge_id, edge in dict_edges.items():
dict_edges[edge_id].start, dict_edges[edge_id].end = str(
edge.start), str(edge.end)
return dict_edges, contig_edges, edges_fpath
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