def extend_scaffold(contig):
visited.add(contig)
scf_name = "ragout-scaffold-{0}".format(counter[0])
counter[0] += 1
scf = Scaffold.with_contigs(scf_name, contig.blocks[0],
contig.blocks[-1], [contig])
scaffolds.append(scf)
#go right
while scf.right in connections:
adjacent = connections[scf.right].end
#print adjacent, contig_index[abs(adjacent)]
assert len(contig_index[abs(adjacent)]) == 1
contig = contig_index[abs(adjacent)][0]
if contig in visited:
break
if contig.blocks[0] == adjacent:
scf.contigs.append(contig)
scf.right = contig.blocks[-1]
visited.add(contig)
continue
if -contig.blocks[-1] == adjacent:
scf.contigs.append(contig)
scf.contigs[-1].sign = -1
scf.right = -contig.blocks[0]
visited.add(contig)
continue
break
#go left
while -scf.left in connections:
adjacent = -connections[-scf.left].end
assert len(contig_index[abs(adjacent)]) == 1
contig = contig_index[abs(adjacent)][0]
if contig in visited:
break
if contig.blocks[-1] == adjacent:
scf.contigs.insert(0, contig)
scf.left = contig.blocks[0]
visited.add(contig)
continue
if -contig.blocks[0] == adjacent:
scf.contigs.insert(0, contig)
scf.contigs[0].sign = -1
scf.left = -contig.blocks[-1]
visited.add(contig)
continue
break
def extend_scaffold(contig):
visited.add(contig)
scf_name = "ragout-scaffold-{0}".format(counter[0])
counter[0] += 1
scf = Scaffold.with_contigs(scf_name, contig.blocks[0], contig.blocks[-1], [contig])
scaffolds.append(scf)
#go right
while scf.right in connections:
adjacent = connections[scf.right].end
#print adjacent, contig_index[abs(adjacent)]
assert len(contig_index[abs(adjacent)]) == 1
contig = contig_index[abs(adjacent)][0]
if contig in visited:
break
if contig.blocks[0] == adjacent:
scf.contigs.append(contig)
scf.right = contig.blocks[-1]
visited.add(contig)
continue
if -contig.blocks[-1] == adjacent:
scf.contigs.append(contig)
scf.contigs[-1].sign = -1
scf.right = -contig.blocks[0]
visited.add(contig)
continue
break
#go left
while -scf.left in connections:
adjacent = -connections[-scf.left].end
assert len(contig_index[abs(adjacent)]) == 1
contig = contig_index[abs(adjacent)][0]
if contig in visited:
break
if contig.blocks[-1] == adjacent:
scf.contigs.insert(0, contig)
scf.left = contig.blocks[0]
visited.add(contig)
continue
if -contig.blocks[0] == adjacent:
scf.contigs.insert(0, contig)
scf.contigs[0].sign = -1
scf.left = -contig.blocks[-1]
visited.add(contig)
continue
break
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 _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 _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 _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 extend_scaffold(contig):
visited.add(contig)
scf_name = "ragout-scaffold-{0}".format(counter[0])
counter[0] += 1
scf = Scaffold.with_contigs(scf_name, contig.left_end(),
contig.right_end(), [contig])
already_complete = (scf.right in adjacencies
and adjacencies[scf.right].block == scf.left
and adjacencies[scf.right].infinity)
if already_complete:
scaffolds.append(scf)
return
#go right
while scf.right in adjacencies and not adjacencies[scf.right].infinity:
adj_block = adjacencies[scf.right].block
adj_distance = adjacencies[scf.right].distance
adj_supporting_genomes = adjacencies[scf.right].supporting_genomes
contig = contig_index[abs(adj_block)]
if contig in visited:
break
if adj_block in [contig.left_end(), contig.right_end()]:
if contig.left_end() == adj_block:
scf.contigs.append(contig)
else:
scf.contigs.append(contig.reverse_copy())
flank = scf.contigs[-2].right_gap() + scf.contigs[-1].left_gap(
)
gap = adj_distance - flank if correct_distances else adj_distance
scf.contigs[-2].link = Link(gap, adj_supporting_genomes)
scf.right = scf.contigs[-1].right_end()
visited.add(contig)
continue
break
#go left
while scf.left in adjacencies and not adjacencies[scf.left].infinity:
adj_block = adjacencies[scf.left].block
adj_distance = adjacencies[scf.left].distance
adj_supporting_genomes = adjacencies[scf.left].supporting_genomes
contig = contig_index[abs(adj_block)]
if contig in visited:
break
if adj_block in [contig.right_end(), contig.left_end()]:
if contig.right_end() == adj_block:
scf.contigs.insert(0, contig)
else:
scf.contigs.insert(0, contig.reverse_copy())
flank = scf.contigs[0].right_gap() + scf.contigs[1].left_gap()
gap = adj_distance - flank if correct_distances else adj_distance
scf.contigs[0].link = Link(gap, adj_supporting_genomes)
scf.left = scf.contigs[0].left_end()
visited.add(contig)
continue
break
if len(scf.contigs) > 1:
scaffolds.append(scf)
def extend_scaffold(contig):
visited.add(contig)
scf_name = "ragout-scaffold-{0}".format(counter[0])
counter[0] += 1
scf = Scaffold.with_contigs(scf_name, contig.left_end(),
contig.right_end(), [contig])
already_complete = (scf.right in adjacencies and
adjacencies[scf.right].block == scf.left and
adjacencies[scf.right].infinity)
if already_complete:
scaffolds.append(scf)
return
#go right
while scf.right in adjacencies and not adjacencies[scf.right].infinity:
adj_block = adjacencies[scf.right].block
adj_distance = adjacencies[scf.right].distance
adj_supporting_genomes = adjacencies[scf.right].supporting_genomes
###KeyError may be throw when ref.indels = False
contig = contig_index[abs(adj_block)]
if contig in visited:
break
if adj_block in [contig.left_end(), contig.right_end()]:
if contig.left_end() == adj_block:
scf.contigs.append(contig)
else:
scf.contigs.append(contig.reverse_copy())
flank = scf.contigs[-2].right_gap() + scf.contigs[-1].left_gap()
try:
gap = adj_distance - flank if correct_distances else adj_distance
except Exception as e:
print scf.right
print adj_distance, flank
scf.contigs[-2].link = Link(gap, adj_supporting_genomes)
scf.right = scf.contigs[-1].right_end()
visited.add(contig)
continue
break
#go left
while scf.left in adjacencies and not adjacencies[scf.left].infinity:
adj_block = adjacencies[scf.left].block
adj_distance = adjacencies[scf.left].distance
adj_supporting_genomes = adjacencies[scf.left].supporting_genomes
contig = contig_index[abs(adj_block)]
if contig in visited:
break
if adj_block in [contig.right_end(), contig.left_end()]:
if contig.right_end() == adj_block:
scf.contigs.insert(0, contig)
else:
scf.contigs.insert(0, contig.reverse_copy())
flank = scf.contigs[0].right_gap() + scf.contigs[1].left_gap()
try:
gap = adj_distance - flank if correct_distances else adj_distance
except Exception as e:
print adj_distance, flank
scf.contigs[0].link = Link(gap, adj_supporting_genomes)
scf.left = scf.contigs[0].left_end()
visited.add(contig)
continue
break
if len(scf.contigs) > 1:
scaffolds.append(scf)
