def parse_spades_output(input_dirpath, output_dirpath, min_edge_len):
gfa_fpath = find_file_by_pattern(input_dirpath, "assembly_graph.gfa")
dict_edges = parse_gfa(gfa_fpath,
min_edge_len,
input_dirpath,
assembler="spades")
contig_edges = parse_spades_paths(input_dirpath, dict_edges)
edges_fpath = get_edges_from_gfa(gfa_fpath, output_dirpath, min_edge_len)
return dict_edges, contig_edges, edges_fpath
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_spades_output(input_dirpath, output_dirpath, min_edge_len):
gfa_fpath = find_file_by_pattern(input_dirpath, "assembly_graph.gfa") or \
find_file_by_pattern(input_dirpath, "assembly_graph_with_scaffolds.gfa")
if not gfa_fpath:
print(
"ERROR! Assembly graph is not found in %s! "
"Please check the folder or specify the file with assembly graph using --graph option"
% (input_dirpath))
sys.exit(1)
dict_edges = parse_gfa(gfa_fpath,
min_edge_len,
input_dirpath,
assembler="spades")
contig_edges = parse_spades_paths(input_dirpath, dict_edges)
edges_fpath = get_edges_from_gfa(gfa_fpath, output_dirpath, min_edge_len)
return dict_edges, contig_edges, edges_fpath
def parse_canu_output(input_dirpath, output_dirpath, min_edge_len):
raw_gfa_fpath = find_file_by_pattern(input_dirpath, ".unitigs.gfa")
if not raw_gfa_fpath:
print("ERROR! GFA file is not found in %s! Please check the options" %
abspath(input_dirpath))
sys.exit(1)
edges_fpath = get_edges_from_gfa(raw_gfa_fpath, output_dirpath,
min_edge_len)
gfa_fpath = join(output_dirpath, basename(raw_gfa_fpath))
if is_empty_file(gfa_fpath) or not can_reuse(
gfa_fpath, files_to_check=[raw_gfa_fpath]):
cmd = 'sed "1s/bogart.edges/1.0/" ' + raw_gfa_fpath
subprocess.call(shlex.split(cmd), stdout=open(gfa_fpath, 'w'))
dict_edges = parse_gfa(gfa_fpath,
min_edge_len,
input_dirpath,
assembler="canu")
contig_edges = parse_canu_assembly_info(input_dirpath, dict_edges)
return dict_edges, contig_edges, edges_fpath