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|
import io, os, sys
import json
import numpy as np
import pprint
import subprocess
import tempfile
from glob import glob
from collections import defaultdict, Counter
from itertools import chain
from Bio import SeqIO, Phylo
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from . import suffix
from .block import Block
from .sequence import Node, Path
from .utils import Strand, as_string, parse_paf, panic, as_record, new_strand, breakpoint
# ------------------------------------------------------------------------
# globals
# WINDOW = 1000
# EXTEND = 2500
pp = pprint.PrettyPrinter(indent=4)
# ------------------------------------------------------------------------
# Junction class
# simple struct
class Junction(object):
def __init__(self, left, right):
self.left = left
self.right = right
def __eq__(self, other):
if self.data == other.data:
return True
elif self.data == other.reverse().data:
return False
else:
return False
def __hash__(self):
return hash(frozenset([self.data, self.reverse().data]))
def __str__(self):
return f"({self.left}, {self.right})"
def __repr__(self):
return str(self)
@property
def data(self):
return ((self.left.blk.id, self.left.strand), (self.right.blk.id, self.right.strand))
@property
def right_id(self):
return self.right.blk.id
@property
def left_id(self):
return self.left.blk.id
@property
def left_blk(self):
return (self.left.blk.id, self.left.strand)
@property
def right_blk(self):
return (self.right.blk.id, self.right.strand)
def reverse(self):
return Junction(
Node(self.right.blk, self.right.num, Strand(-1*self.right.strand)),
Node(self.left.blk, self.left.num, Strand(-1*self.left.strand)),
)
def rev_blk(b):
return (b[0], Strand(-1*b[1]))
# ------------------------------------------------------------------------
# Graph class
class Graph(object):
"""docstring for Graph"""
def __init__(self):
self.name = "" # The name of graph. Will be used as file basename in exports
self.blks = {} # All blocks/alignments
self.seqs = {} # All sequences (as list of blocks)
self.sfxt = None # Suffix tree of block records
self.dmtx = None # Graph distance matrix
# --- Class methods ---
@classmethod
def from_seq(cls, name, seq):
newg = cls()
blk = Block.from_seq(name, seq)
newg.name = name
newg.blks = {blk.id : blk}
newg.seqs = {name : Path(name, Node(blk, 0, Strand.Plus), 0)}
return newg
@classmethod
def from_dict(cls, d):
G = Graph()
G.name = d['name']
G.blks = [Block.from_dict(b) for b in d['blocks']]
G.blks = {b.id : b for b in G.blks}
G.seqs = [Path.from_dict(seq, G.blks) for seq in d['seqs']]
G.seqs = {p.name : p for p in G.seqs}
G.sfxt = None
G.dmtx = None
if d['suffix'] is not None:
G.compile_suffix()
G.dmtx = d['distmtx']
return G
@classmethod
def connected_components(cls, G):
# -----------------------------
# internal functions
def overlaps(s1, s2):
return len(s1.intersection(s2)) > 0
def component(graph, name):
cc = Graph()
cc.blks = {id:G.blks.pop(id) for id in graph}
cc.seqs = {nm:G.seqs.pop(nm) for nm in name}
cc.sfxt = None
cc.dmtx = None
return cc
# -----------------------------
# main body
graphs, names = [], []
for name, path in G.seqs.items():
blks = set([b.id for b in path.blocks()])
gi = [i for i, g in enumerate(graphs) if overlaps(blks, g)]
if len(gi) == 0:
graphs.append(blks)
names.append(set([name]))
continue
graphs[gi[0]] = graphs[gi[0]].union(blks, *(graphs.pop(i) for i in gi[:0:-1]))
names[gi[0]] = names[gi[0]].union(set([name]), *(names.pop(i) for i in gi[:0:-1]))
return [component(graph, name) for graph, name in zip(graphs, names)]
@classmethod
def fuse(cls, g1, g2):
ng = Graph()
combine = lambda d1, d2: {**d1, **d2}
ng.blks = combine(g1.blks, g2.blks)
ng.seqs = combine(g1.seqs, g2.seqs)
return ng
# ---------------
# methods
def union(self, qpath, rpath, out, cutoff=0, alpha=10, beta=2, extensive=False, edge_window=1000, edge_extend=2500):
from seqanpy import align_global as align
# ----------------------------------
# internal functions
def energy(hit):
l = hit["aligned_bases"]
if l <= cutoff:
return l
num = lambda k: len(self.blks[hit[k]["name"]].muts)
cuts = lambda k: (hit[k]['start'] > cutoff) + ((hit[k]['len']-hit[k]['end']) > cutoff)
if extensive:
delP = num('qry')*cuts('qry') + num('ref')*cuts('ref')
else:
delP = cuts('qry') + cuts('ref')
dmut = hit["aligned_length"] * hit["divergence"]
return -l + alpha*delP + beta*dmut
def accepted(hit):
return energy(hit) < 0
if cutoff <= 0:
def proc(hit):
return hit
else:
def proc(hit):
# -----------------------
# load in sequences
with open(f"{qpath}.fa", 'r') as fd:
qfa = {s.id:str(s.seq) for s in SeqIO.parse(fd, 'fasta')}
if qpath == rpath:
rfa = qfa
else:
with open(f"{rpath}.fa", 'r') as fd:
rfa = {s.id:str(s.seq) for s in SeqIO.parse(fd, 'fasta')}
# -----------------------
# internal functions
def to_cigar(aln):
cigar = ""
s1, s2 = np.fromstring(aln[0], dtype=np.int8), np.fromstring(aln[1], dtype=np.int8)
M, I, D = 0, 0, 0
for (c1, c2) in zip(s1, s2):
if c1 == ord("-") and c2 == ord("-"):
breakpoint("panic")
elif c1 == ord("-"):
if I > 0:
cigar += f"{I}I"
I = 0
elif M > 0:
cigar += f"{M}M"
M = 0
D += 1
elif c2 == ord("-"):
if D > 0:
cigar += f"{D}D"
D = 0
elif M > 0:
cigar += f"{M}M"
M = 0
I += 1
else:
if D > 0:
cigar += f"{D}D"
D = 0
elif I > 0:
cigar += f"{I}I"
I = 0
M += 1
if I > 0:
cigar += f"{I}I"
I = 0
elif M > 0:
cigar += f"{M}M"
M = 0
elif D > 0:
cigar += f"{D}D"
M = 0
return cigar
def revcmpl_if(s, cond):
if cond:
return str(Seq.reverse_complement(Seq(s)))
else:
return s
def get_seqs():
return qfa[hit['qry']['name']], rfa[hit['ref']['name']]
# -----------------------
# body
dS_q = hit['qry']['start']
dE_q = hit['qry']['len'] - hit['qry']['end']
dS_r = hit['ref']['start']
dE_r = hit['ref']['len'] - hit['ref']['end']
# Left side of match
if 0 < dS_q <= cutoff and (dS_r > cutoff or dS_r == 0):
hit['cigar'] = f"{dS_q}I" + hit['cigar']
hit['qry']['start'] = 0
elif 0 < dS_r <= cutoff and (dS_q > cutoff or dS_q == 0):
hit['cigar'] = f"{dS_r}D" + hit['cigar']
hit['ref']['start'] = 0
elif 0 < dS_q <= cutoff and 0 < dS_r <= cutoff:
qseq, rseq = get_seqs()
aln = align(revcmpl_if(qseq, hit['orientation']==Strand.Minus)[0:dS_q], rseq[0:dS_r])[1:]
hit['cigar'] = to_cigar(aln) + hit['cigar']
hit['qry']['start'] = 0
hit['ref']['start'] = 0
hit['aligned_bases'] += len(aln[0])
# Right side of match
if 0 < dE_q <= cutoff and (dE_r > cutoff or dE_r == 0):
hit['cigar'] += f"{dE_q}I"
hit['qry']['end'] = hit['qry']['len']
elif 0 < dE_r <= cutoff and (dE_q > cutoff or dE_q == 0):
hit['cigar'] += f"{dE_r}D"
hit['ref']['end'] = hit['ref']['len']
elif 0 < dE_q <= cutoff and 0 < dE_r <= cutoff:
qseq, rseq = get_seqs()
aln = align(revcmpl_if(qseq, hit['orientation']==Strand.Minus)[-dE_q:], rseq[-dE_r:])[1:]
hit['cigar'] = hit['cigar'] + to_cigar(aln)
hit['qry']['end'] = hit['qry']['len']
hit['ref']['end'] = hit['ref']['len']
hit['aligned_bases'] += len(aln[0])
return hit
# ----------------------------------
# body
os.system(f"minimap2 -t 2 -x asm20 -m 10 -n 2 -s 30 -D -c {rpath}.fa {qpath}.fa 1>{out}.paf 2>log")
with open(f"{out}.paf") as fd:
paf = parse_paf(fd)
paf.sort(key = lambda x: energy(x))
merged_blks = set()
if len(paf) == 0:
return self, False
merged = False
for hit in paf:
if hit['qry']['name'] in merged_blks \
or hit['ref']['name'] in merged_blks \
or(hit['ref']['name'] <= hit['qry']['name'] and qpath == rpath) \
or not accepted(hit):
continue
merged = True
self.merge(proc(hit), edge_window, edge_extend)
merged_blks.add(hit['ref']['name'])
merged_blks.add(hit['qry']['name'])
self.remove_transitives()
for path in self.seqs.values():
path.rm_nil_blks()
return self, merged
# a junction is a pair of adjacent blocks.
def junctions(self):
junctions = defaultdict(list)
for iso, path in self.seqs.items():
if len(path.nodes) == 1:
continue
for i, n in enumerate(path.nodes):
j = Junction(path.nodes[i-1], n)
junctions[j].append(iso)
return { k:dict(Counter(v)) for k, v in junctions.items() }
def remove_transitives(self):
js = self.junctions()
transitives = []
for j, isos in js.items():
left_eq_right = self.blks[j.left.blk.id].isolates == self.blks[j.right.blk.id].isolates
left_eq_isos = isos == self.blks[j.left.blk.id].isolates
if left_eq_right and left_eq_isos:
transitives.append(j)
chains = {}
for j in transitives:
if j.left_id in chains and j.right_id in chains:
c1, c2 = chains[j.left_id], chains[j.right_id]
if c1 == c2:
continue
if j.left_blk==c1[-1] and j.right_blk==c2[0]:
new_chain = c1 + c2
elif j.left_blk==c1[-1] and rev_blk(j.right_blk)==c2[-1]:
new_chain = c1 + [rev_blk(b) for b in c2[::-1]]
elif rev_blk(j.left_blk)==c1[0] and j.right_blk==c2[0]:
new_chain = [rev_blk(b) for b in c1[::-1]] + c2
elif rev_blk(j.left_blk)==c1[0] and rev_blk(j.right_blk)==c2[-1]:
new_chain = c2 + c1
else:
breakpoint("case not covered")
for b, _ in new_chain:
chains[b] = new_chain
elif j.left_id in chains:
c = chains[j.left_id]
if j.left_blk == c[-1]:
c.append(j.right_blk)
elif rev_blk(j.left_blk) == c[0]:
c.insert(0, rev_blk(j.right_blk))
else:
breakpoint("chains should be linear")
elif j.right_id in chains:
c = chains[j.right_id]
if j.right_blk == c[-1]:
c.append(rev_blk(j.left_blk))
elif j.right_blk == c[0]:
c.insert(0, j.left_blk)
else:
breakpoint("chains should be linear")
else:
chains[j.left_id] = [j.left_blk, j.right_blk]
chains[j.right_id] = chains[j.left_id]
chains = list({id(c):c for c in chains.values()}.values())
for c in chains:
new_blk = Block.cat([self.blks[b] if s == Strand.Plus else self.blks[b].rev_cmpl() for b, s in c])
# TODO: check that isos is constant along the chain
for iso in self.blks[c[0][0]].isolates.keys():
self.seqs[iso].merge(c[0], c[-1], new_blk)
self.blks[new_blk.id] = new_blk
for b, _ in c:
self.blks.pop(b)
def prune_blks(self):
blks = set()
for path in self.seqs.values():
blks.update(path.blocks())
self.blks = {b.id:self.blks[b.id] for b in blks}
def merge(self, hit, window, extend):
old_ref = self.blks[hit['ref']['name']]
old_qry = self.blks[hit['qry']['name']]
# As we slice here, we DONT need to remember the starting position.
# This is why in from_aln(aln) we set the start index to 0
ref = old_ref[hit['ref']['start']:hit['ref']['end']]
qry = old_qry[hit['qry']['start']:hit['qry']['end']]
if hit["orientation"] == Strand.Minus:
qry = qry.rev_cmpl()
aln = {"ref_seq" : as_string(ref.seq),
"qry_seq" : as_string(qry.seq),
"cigar" : hit["cigar"],
"ref_cluster" : ref.muts,
"qry_cluster" : qry.muts,
"ref_start" : hit["ref"]["start"],
"ref_name" : hit["ref"]["name"],
"qry_start" : hit["qry"]["start"],
"qry_name" : hit["qry"]["name"],
"orientation" : hit["orientation"]}
merged_blks, new_qrys, new_refs, shared_blks, blk_map = Block.from_aln(aln)
for merged_blk in merged_blks:
self.blks[merged_blk.id] = merged_blk
def update(blk, add_blks, hit, strand):
new_blks = []
# The convention for the tuples are (block, strand orientation, merged)
if hit['start'] > 0:
left = blk[0:hit['start']]
self.blks[left.id] = left
new_blks.append((left, Strand.Plus, False))
for b in add_blks:
new_blks.append((b, strand, True))
if hit['end'] < len(blk):
right = blk[hit['end']:]
self.blks[right.id] = right
new_blks.append((right, Strand.Plus, False))
for tag in blk.muts.keys():
path = self.seqs[tag[0]]
path.replace(blk, tag, new_blks, blk_map)
return new_blks
new_blocks = []
new_blocks.extend(update(old_ref, new_refs, hit['ref'], Strand.Plus))
new_blocks.extend(update(old_qry, new_qrys, hit['qry'], hit['orientation']))
lblks_set_x, rblks_set_x = set(), set()
lblks_set_s, rblks_set_s = set(), set()
first = True
num_seqs = 0
for tag in shared_blks[0].muts.keys():
pos = [self.seqs[tag[0]].position_of(b, tag[1]) for b in shared_blks]
strand = [self.seqs[tag[0]].orientation_of(b, tag[1]) for b in shared_blks]
beg, end = pos[0], pos[-1]
if strand[0] == Strand.Plus:
lwindow = min(window, shared_blks[0].len_of(*tag))
rwindow = min(window, shared_blks[-1].len_of(*tag))
lblks_x = self.seqs[tag[0]][beg[0]-extend:beg[0]+lwindow]
rblks_x = self.seqs[tag[0]][end[1]-rwindow:end[1]+extend]
# lblks_s = self.seqs[tag[0]][beg[0]:beg[0]+window]
# rblks_s = self.seqs[tag[0]][end[1]-window:end[1]]
elif strand[0] == Strand.Minus:
lwindow = min(window, shared_blks[-1].len_of(*tag))
rwindow = min(window, shared_blks[0].len_of(*tag))
rblks_x = self.seqs[tag[0]][beg[0]-extend:beg[0]+rwindow]
lblks_x = self.seqs[tag[0]][end[1]-lwindow:end[1]+extend]
# rblks_s = self.seqs[tag[0]][beg[0]:beg[0]+window]
# lblks_s = self.seqs[tag[0]][end[1]-window:end[1]]
else:
raise ValueError("unrecognized strand polarity")
if first:
lblks_set_x = set([b.id for b in lblks_x])
rblks_set_x = set([b.id for b in rblks_x])
# lblks_set_s = set([b.id for b in lblks_s])
# rblks_set_s = set([b.id for b in rblks_s])
lblks_set_s = set([b.id for b in lblks_x])
rblks_set_s = set([b.id for b in rblks_x])
first = False
else:
lblks_set_x.intersection_update(set([b.id for b in lblks_x]))
rblks_set_x.intersection_update(set([b.id for b in rblks_x]))
lblks_set_s.update(set([b.id for b in lblks_x]))
rblks_set_s.update(set([b.id for b in rblks_x]))
# lblks_set_s.intersection_update(set([b.id for b in lblks_s]))
# rblks_set_s.intersection_update(set([b.id for b in rblks_s]))
num_seqs += 1
def emit(side):
if side == 'left':
delta = len(lblks_set_s)-len(lblks_set_x)
elif side == 'right':
delta = len(lblks_set_s)-len(rblks_set_x)
else:
raise ValueError(f"unrecognized argument '{side}' for side")
if delta > 0 and num_seqs > 1:
print(f">LEN={delta}", end=';')
try:
fd, path = tempfile.mkstemp()
with os.fdopen(fd, 'w') as tmp:
for i, tag in enumerate(merged_blks[0].muts.keys()):
pos = [self.seqs[tag[0]].position_of(b, tag[1]) for b in shared_blks]
strand = [self.seqs[tag[0]].orientation_of(b, tag[1]) for b in shared_blks]
beg, end = pos[0], pos[-1]
if strand[0] == Strand.Plus:
if side == 'left':
left, right = beg[0]-extend,beg[0]+min(window,shared_blks[0].len_of(*tag))
elif side == 'right':
left, right = end[1]-min(window,shared_blks[-1].len_of(*tag)),end[1]+extend
else:
raise ValueError(f"unrecognized argument '{side}' for side")
elif strand[0] == Strand.Minus:
if side == 'left':
left, right = end[1]-min(window,shared_blks[-1].len_of(*tag)),end[1]+extend
elif side == 'right':
left, right = beg[0]-extend,beg[0]+min(window, shared_blks[0].len_of(*tag))
else:
raise ValueError(f"unrecognized argument '{side}' for side")
iso_blks = self.seqs[tag[0]][left:right]
print("POSITIONS", pos)
print("STRAND", strand)
print("LIST", shared_blks)
print("MERGED", merged_blks)
print("INTERSECTION", lblks_set_x if side == 'left' else rblks_set_x)
print("UNION", lblks_set_s if side == 'left' else rblks_set_s)
print("ISO", iso_blks)
breakpoint("stop")
tmp.write(f">isolate_{i:04d} {','.join(b.id for b in iso_blks)}\n")
s = self.seqs[tag[0]].sequence_range(left,right)
if len(s) > extend + window:
breakpoint(f"bad sequence slicing: {len(s)}")
tmp.write(s + '\n')
tmp.flush()
proc = [None, None]
out = [None, None]
err = [None, None]
proc[0] = subprocess.Popen(f"mafft --auto {path}",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
proc[1] = subprocess.Popen(f"fasttree",
stdin =subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
out[0], err[0] = proc[0].communicate()
out[1], err[1] = proc[1].communicate(input=out[0])
tree = Phylo.read(io.StringIO(out[1].decode('utf-8')), format='newick')
print(f"ALIGNMENT=\n{out[0]}", end=";")
print(f"SCORE={tree.total_branch_length()/(2*num_seqs)}", end=";")
print("\n", end="")
finally:
os.remove(path)
else:
print(f">NO MATCH")
emit('left')
emit('right')
self.prune_blks()
return [b[0] for b in new_blocks]
def extract(self, name, strip_gaps=True, verbose=False):
seq = self.seqs[name].sequence()
if strip_gaps:
seq = seq.replace('-', '')
return seq
def compress_ratio(self, extensive=False, name=None):
unc = 0
if name is None:
for n in self.seqs:
seq = self.extract(n)
unc += len(seq)
cmp = np.sum([len(x) for x in self.blks.values()])
else:
cmp = np.sum([len(x) for x in self.blks.values() if name in x.muts])
return unc/cmp/len(self.seqs) if not extensive else unc/cmp
def contains(self, other):
return set(other.seqs.keys()).issubset(set(self.seqs.keys()))
def compile_suffix(self, force=False):
if self.sfxt is None or force:
self.sfxt = suffix.Tree({k: [c[0:2] for c in v] for k, v in self.seqs.items()})
def compute_pdist(self, force=False):
if self.dmtx is None or force:
nms, N = sorted(list(self.seqs.keys())), len(self.seqs)
self.dmtx = np.zeros((N*(N-1))//2)
n = 0
for i, nm1 in enumerate(nms):
for nm2 in nms[:i]:
self.dmtx[n] = len(self.sfxt.matches(nm1, nm2))
n += 1
def to_json(self, wtr, minlen=500):
J = {}
cleaned_seqs = {s:[b for b in self.seqs[s] if len(self.blks[b[0]])>minlen]
for s in self.seqs}
relevant_blocks = set()
for s in cleaned_seqs.values():
relevant_blocks.update([b[0] for b in s])
J['Isolate_names'] = list(cleaned_seqs.keys())
J['Plasmids'] = [[x for x in cleaned_seqs[s]] for s in J['Isolate_names']]
# Build node substructure
nodes = {}
for b in relevant_blocks:
aln = { J["Isolate_names"].index(iso) :
self.blks[b].extract(iso, num, strip_gaps=False) for iso, num in self.blks[b].muts }
nodes[b] = {"ID" : b,
"Genomes" : {"Consensus" : ''.join(self.blks[b].seq),
"Alignment" : aln },
"Out_Edges" : [],
"In_Edges" : []}
# Gather edges (node/node junctions) for each node
edges = {}
for pname, p in zip(range(len(J["Isolate_names"])), J['Plasmids']):
for i in range(len(p)-1):
e = (p[i], p[i+1])
if e in edges:
edges[e]["Isolates"].append(pname)
else:
edges[e] = {"Source" : e[0], "Target" : e[1], "Isolates" : [pname]}
e = (p[-1], p[0])
if e in edges:
edges[e]["Isolates"].append(pname)
else:
edges[e] = {"Source" : e[0], "Target" : e[1], "Isolates" : [pname]}
for e in edges:
nodes[e[0][0]]["Out_Edges"].append(edges[e])
nodes[e[1][0]]["In_Edges"].append(edges[e])
J["Nodes"] = nodes
json.dump(J, wtr)
def to_dict(self):
return {'name' : self.name,
'seqs' : [s.to_dict() for s in self.seqs.values()],
'blocks' : [b.to_dict() for b in self.blks.values()],
'suffix' : None if self.sfxt is None else "compiled",
'distmtx': self.dmtx}
def write_fasta(self, wtr):
SeqIO.write(sorted([ as_record(as_string(c.seq), c.id) for c in self.blks.values() ],
key=lambda x: len(x), reverse=True), wtr, format='fasta')
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