def _insert_from_graph_experement(graph_file, scaffolds_in, max_path_len):
new_scaffolds = []
graph = _load_dot(graph_file)
ordered_contigs = set()
for scf in scaffolds_in:
ordered_contigs |= set(map(lambda s: s.name, scf.contigs))
for scf in scaffolds_in:
new_scaffolds.append(Scaffold(scf.name))
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
new_scaffolds[-1].contigs.append(prev_cont)
#find unique path
path_nodes = _get_unigue_path_experiment(graph, prev_cont, new_cont,
max_path_len, ordered_contigs)
if not path_nodes:
continue
#insert contigs along the path
for node in path_nodes:
new_scaffolds[-1].contigs.append(Contig.from_sting(node))
new_scaffolds[-1].contigs.append(new_cont)
return new_scaffolds
def _update_scaffolds(scaffolds, perm_container):
"""
Updates scaffolds wrt to given permutations
"""
perm_index = defaultdict(list)
for perm in perm_container.target_perms:
perm_index[(perm.chr_name, perm.repeat_id)].append(perm)
new_scaffolds = []
for scf in scaffolds:
new_contigs = []
for contig in scf.contigs:
inner_perms = []
for new_perm in perm_index[(contig.perm.chr_name,
contig.perm.repeat_id)]:
if (contig.perm.seq_start <= new_perm.seq_start <
contig.perm.seq_end):
inner_perms.append(new_perm)
assert (contig.perm.seq_start < new_perm.seq_end <=
contig.perm.seq_end)
if not inner_perms:
logger.debug("Lost: %s", str(contig.perm))
continue
inner_perms.sort(key=lambda p: p.seq_start,
reverse=contig.sign < 0)
for prev_perm, next_perm in zip(inner_perms[:-1], inner_perms[1:]):
if contig.sign > 0:
gap_length = next_perm.seq_start - prev_perm.seq_end
else:
gap_length = prev_perm.seq_start - next_perm.seq_end
support = [
GenChrPair(prev_perm.genome_name, prev_perm.chr_name)
]
new_contigs.append(
Contig.with_perm(prev_perm, contig.sign,
Link(gap_length, support)))
new_contigs.append(
Contig.with_perm(inner_perms[-1], contig.sign,
copy(contig.link)))
if len(new_contigs):
new_scaffolds.append(
Scaffold.with_contigs(scf.name, None, None, new_contigs))
return new_scaffolds
def _merge_consecutive_contigs(scaffolds):
"""
Merges consecutive contig fragments originating from a same contig
"""
new_scaffolds = []
num_contigs = 0
for scf in scaffolds:
new_contigs = []
cur_sign, cur_perm, cur_link = None, None, None
for cnt in scf.contigs:
consistent = False
if cur_sign == cnt.sign and cnt.perm.chr_name == cur_perm.chr_name:
if cur_sign > 0 and cur_perm.seq_end == cnt.perm.seq_start:
cur_perm.seq_end = cnt.perm.seq_end
cur_perm.blocks.extend(cnt.perm.blocks)
consistent = True
if cur_sign < 0 and cur_perm.seq_start == cnt.perm.seq_end:
cur_perm.seq_start = cnt.perm.seq_start
cur_perm.blocks = cnt.perm.blocks + cur_perm.blocks
consistent = True
if not consistent:
if cur_perm:
new_contigs.append(
Contig.with_perm(cur_perm, cur_sign, cur_link))
cur_perm = deepcopy(cnt.perm)
cur_sign = cnt.sign
cur_link = cnt.link
if cur_perm:
new_contigs.append(Contig.with_perm(cur_perm, cur_sign, cur_link))
num_contigs += len(new_contigs)
new_scaffolds.append(
Scaffold.with_contigs(scf.name, None, None, new_contigs))
logger.debug("Merging consequtive contigs: %d left", num_contigs)
return new_scaffolds
def _merge_consecutive_contigs(scaffolds):
"""
Merges consecutive contig fragments originating from a same contig
"""
new_scaffolds = []
num_contigs = 0
for scf in scaffolds:
new_contigs = []
cur_sign, cur_perm, cur_link = None, None, None
for cnt in scf.contigs:
consistent = False
if cur_sign == cnt.sign and cnt.perm.chr_name == cur_perm.chr_name:
if cur_sign > 0 and cur_perm.seq_end == cnt.perm.seq_start:
cur_perm.seq_end = cnt.perm.seq_end
cur_perm.blocks.extend(cnt.perm.blocks)
consistent = True
if cur_sign < 0 and cur_perm.seq_start == cnt.perm.seq_end:
cur_perm.seq_start = cnt.perm.seq_start
cur_perm.blocks = cnt.perm.blocks + cur_perm.blocks
consistent = True
if not consistent:
if cur_perm:
new_contigs.append(Contig.with_perm(cur_perm, cur_sign, cur_link))
cur_perm = deepcopy(cnt.perm)
cur_sign = cnt.sign
cur_link = cnt.link
if cur_perm:
new_contigs.append(Contig.with_perm(cur_perm, cur_sign, cur_link))
num_contigs += len(new_contigs)
new_scaffolds.append(Scaffold.with_contigs(scf.name, None,
None, new_contigs))
logger.debug("Merging consequtive contigs: {0} left".format(num_contigs))
return new_scaffolds
def _make_contigs(perm_container):
"""
A helper function to make Contig structures
"""
contigs = []
index = {}
for perm in perm_container.target_perms:
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
return contigs, index
def _make_contigs(perm_container, ancestral=False):
"""
A helper function to make Contig structures
"""
contigs = []
index = {}
if not ancestral:
for perm in perm_container.target_perms:
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
else:
for perm in perm_container.ancestor_perms:
#print idx
#print perm.name(), [block.block_id for block in perm.blocks]
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
return contigs, index
def _make_contigs(perm_container):
contigs = []
index = defaultdict(list)
for perm in perm_container.target_perms_filtered:
if len(perm.blocks) == 0:
continue
contigs.append(Contig(perm.chr_id))
contigs[-1].blocks = copy.copy(perm.blocks)
for block in perm.blocks:
index[abs(block)].append(contigs[-1])
return contigs, index
def _make_contigs(perm_container):
"""
A helper function to make Contig structures
"""
contigs = []
index = {}
for perm in perm_container.target_perms:
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
return contigs, index
def _make_contigs(perm_container, ancestral=False):
"""
A helper function to make Contig structures
"""
contigs = []
index = {}
if not ancestral:
for perm in perm_container.target_perms:
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
else:
for perm in perm_container.ancestor_perms:
#print idx
#print perm.name(), [block.block_id for block in perm.blocks]
assert len(perm.blocks)
contigs.append(Contig.with_perm(perm))
for block in perm.blocks:
assert block.block_id not in index
index[block.block_id] = contigs[-1]
return contigs, index
def _insert_from_graph(graph, scaffolds_in, max_path_len, contigs_fasta):
"""
Inserts contigs from the assembly graph into scaffolds
"""
new_scaffolds = []
ordered_contigs = set()
for scf in scaffolds_in:
ordered_contigs |= set([c.name() for c in scf.contigs])
reverse_graph = graph.reverse()
for scf in scaffolds_in:
new_scaffolds.append(Scaffold(scf.name))
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
new_scaffolds[-1].contigs.append(prev_cont)
#find contigs to insert
path_nodes = _get_cut_vertices(graph, reverse_graph, prev_cont,
new_cont, max_path_len,
ordered_contigs)
if not path_nodes:
continue
#insert contigs along the path
supp_genomes = prev_cont.link.supporting_genomes
prev_cont.link.supporting_assembly = True
prev_cont.link.gap = config.vals["min_scaffold_gap"]
for node in path_nodes:
sign = 1 if node[0] == "+" else -1
name = node[1:]
new_contig = Contig.with_sequence(name,
len(contigs_fasta[name]),
sign)
new_contig.link.supporting_assembly = True
new_contig.link.gap = config.vals["min_scaffold_gap"]
new_contig.link.supporting_genomes = supp_genomes
new_scaffolds[-1].contigs.append(new_contig)
new_scaffolds[-1].contigs.append(scf.contigs[-1])
return new_scaffolds
def _update_scaffolds(scaffolds, perm_container, ancestral=False):
"""
Updates scaffolds wrt to given permutations
"""
perm_index = defaultdict(list)
if not ancestral:
for perm in perm_container.target_perms:
perm_index[(perm.chr_name, perm.repeat_id)].append(perm)
else:
for perm in perm_container.ancestor_perms:
perm_index[(perm.chr_name, perm.repeat_id)].append(perm)
new_scaffolds = []
for scf in scaffolds:
new_contigs = []
for contig in scf.contigs:
inner_perms = []
for new_perm in perm_index[(contig.perm.chr_name,
contig.perm.repeat_id)]:
if (contig.perm.seq_start <= new_perm.seq_start <
contig.perm.seq_end):
inner_perms.append(new_perm)
assert (contig.perm.seq_start < new_perm.seq_end <=
contig.perm.seq_end)
if not inner_perms:
logger.debug("Lost: {0}".format(contig.perm))
continue
inner_perms.sort(key=lambda p: p.seq_start,
reverse=contig.sign < 0)
gap_length = contig.link.gap
for new_perm in inner_perms:
gap_length -= new_perm.length()
new_link = Link(gap_length, contig.link.supporting_genomes)
new_contigs.append(
Contig.with_perm(new_perm, contig.sign, new_link))
new_contigs[-1].link = contig.link
new_scaffolds.append(
Scaffold.with_contigs(scf.name, None, None, new_contigs))
return new_scaffolds
def _insert_from_graph(graph, scaffolds_in, max_path_len, contigs_fasta):
"""
Inserts contigs from the assembly graph into scaffolds
"""
new_scaffolds = []
ordered_contigs = set()
for scf in scaffolds_in:
ordered_contigs |= set(map(lambda c: c.name(), scf.contigs))
reverse_graph = graph.reverse()
for scf in scaffolds_in:
new_scaffolds.append(Scaffold(scf.name))
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
new_scaffolds[-1].contigs.append(prev_cont)
#find contigs to insert
path_nodes = _get_cut_vertices(graph, reverse_graph, prev_cont,
new_cont, max_path_len,
ordered_contigs)
if not path_nodes:
continue
#insert contigs along the path
supp_genomes = prev_cont.link.supporting_genomes
prev_cont.link.supporting_assembly = True
prev_cont.link.gap = config.vals["min_scaffold_gap"]
for node in path_nodes:
sign = 1 if node[0] == "+" else -1
name = node[1:]
new_contig = Contig.with_sequence(name,
len(contigs_fasta[name]), sign)
new_contig.link.supporting_assembly = True
new_contig.link.gap = config.vals["min_scaffold_gap"]
new_contig.link.supporting_genomes = supp_genomes
new_scaffolds[-1].contigs.append(new_contig)
new_scaffolds[-1].contigs.append(scf.contigs[-1])
return new_scaffolds
def _update_scaffolds(scaffolds, perm_container, ancestral=False):
"""
Updates scaffolds wrt to given permutations
"""
perm_index = defaultdict(list)
if not ancestral:
for perm in perm_container.target_perms:
perm_index[(perm.chr_name, perm.repeat_id)].append(perm)
else:
for perm in perm_container.ancestor_perms:
perm_index[(perm.chr_name, perm.repeat_id)].append(perm)
new_scaffolds = []
for scf in scaffolds:
new_contigs = []
for contig in scf.contigs:
inner_perms = []
for new_perm in perm_index[(contig.perm.chr_name,
contig.perm.repeat_id)]:
if (contig.perm.seq_start <= new_perm.seq_start
< contig.perm.seq_end):
inner_perms.append(new_perm)
assert (contig.perm.seq_start < new_perm.seq_end
<= contig.perm.seq_end)
if not inner_perms:
logger.debug("Lost: {0}".format(contig.perm))
continue
inner_perms.sort(key=lambda p: p.seq_start, reverse=contig.sign < 0)
gap_length = contig.link.gap
for new_perm in inner_perms:
gap_length -= new_perm.length()
new_link = Link(gap_length, contig.link.supporting_genomes)
new_contigs.append(Contig.with_perm(new_perm, contig.sign,
new_link))
new_contigs[-1].link = contig.link
new_scaffolds.append(Scaffold.with_contigs(scf.name, None,
None, new_contigs))
return new_scaffolds
def _insert_from_graph(graph_file, scaffolds_in, max_path_len):
new_scaffolds = []
graph = _load_dot(graph_file)
logger.debug("Loaded overlap graph with {0} nodes".format(len(graph)))
ordered_contigs = set()
for scf in scaffolds_in:
ordered_contigs |= set(map(lambda s: s.name, scf.contigs))
for scf in scaffolds_in:
new_scaffolds.append(Scaffold(scf.name))
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
new_scaffolds[-1].contigs.append(prev_cont)
#find unique path
path_nodes = _get_unique_path(graph, prev_cont,
new_cont, max_path_len)
if not path_nodes:
continue
#check path consistency
consistent = True
for node in path_nodes:
if node[1:] in ordered_contigs:
logger.debug("Path inconsistency {0} -- {1}: {2}"
.format(prev_cont, new_cont, node))
consistent = False
break
if not consistent:
continue
#insert contigs along the path
for node in path_nodes:
new_scaffolds[-1].contigs.append(Contig.from_sting(node))
new_scaffolds[-1].contigs.append(new_cont)
return new_scaffolds
def merge(big_scaffolds, small_scaffolds):
logger.info("Merging two iterations")
big_index = set()
for scf in big_scaffolds:
for c in scf.contigs:
big_index.add(c.name)
small_index = {}
for scf in small_scaffolds:
for pos, contig in enumerate(scf.contigs):
assert contig.name not in small_index
small_index[contig.name] = (scf, pos)
count = 0
new_scafflods = []
for scf in big_scaffolds:
result = []
for prev_cont, new_cont in zip(scf.contigs[:-1], scf.contigs[1:]):
result.append(prev_cont)
try:
scf_prev, begin = small_index[prev_cont.name]
scf_new, end = small_index[new_cont.name]
except KeyError:
continue
if scf_prev.name != scf_new.name:
continue
assert end != begin
same_dir = True
if end < begin:
same_dir = False
end, begin = begin, end
consistent = True
for c in scf_prev.contigs[begin + 1:end]:
if c.name in big_index:
consistent = False
break
if not consistent or end - begin == 1:
continue
if ((prev_cont.sign == new_cont.sign) !=
(scf_prev.contigs[begin].sign == scf_prev.contigs[end].sign)):
continue
count += end - begin - 1
contigs = scf_prev.contigs[begin + 1:end]
if not same_dir:
contigs = contigs[::-1]
contigs = list(
map(lambda c: Contig(c.name, -c.sign, 0), contigs))
result.extend(contigs)
result.append(new_cont)
s = Scaffold(scf.name)
s.contigs = result
new_scafflods.append(s)
return new_scafflods
