def scaffold(args):
logging.info('Creating the scaffold graph')
g = load_from_fasta_tsv(args.fasta, args.edges, args.containment)
print_stats(g)
# delete small vertices
if args.min_ctg_len:
logging.info('Removing vertices smaller than %d bp' % args.min_ctg_len)
n_removed = 0
for v in g.vertices:
if len(v.seq) < args.min_ctg_len:
g.remove_vertex(v)
n_removed += 1
logging.info('Removed %d vertices' % n_removed)
print_stats(g)
# prune scaffold edges
if g.edges:
logging.info('Simplifying the graph using paired-end reads')
logging.info('Contracting unambigous paths')
contract_edges(g, store_ordering=True)
print_stats(g)
save_fasta(g, 'contracted.fasta')
if args.cut_tip_len:
n_cut = cut_tips(g, d=args.cut_tip_len)
logging.info('Cut %d tips shorter than %d bp' \
% (n_cut, args.cut_tip_len))
logging.info('Pruning edges with low support')
n_pruned1 = prune_scaffold_edges(g, abs_support_thr=args.pe_abs_thr,
rel_support_thr=args.pe_rel_thr)
n_pruned2 = prune_scaffold_edges_via_wells(g, thr=args.pe_rc_rel_thr)
logging.info('%d edges pruned' % (n_pruned1 + n_pruned2))
logging.info('Contracting unambigous paths')
n_contracted = contract_edges(g)
print_stats(g)
# delete all existing edges from the graph
E = g.edges
for e in E:
g.remove_edge(e)
# create new edges whenever vertices have similar well profiles
logging.info('Creating edges from read clouds')
n_edges = make_wellscaff_edges(g, min_common=args.rc_abs_thr,
min_thr=args.rc_rel_edge_thr)
logging.info('%d scaffold edges from read clouds' % n_edges)
logging.info('Auto-saving graph with prefix %s.wellscaff' % args.out)
save_to_fasta_tsv(g, '%s.wellscaff.fasta' % args.out,
'%s.wellscaff.tsv' % args.out,
'%s.wellscaff.containment' % args.out)
logging.info('Pruning edges with low support')
n_pruned = prune_via_wells(g, min_common=args.rc_abs_thr,
min_thr=args.rc_rel_prun_thr)
logging.info('%d edges pruned' % n_pruned)
logging.info('Contracting unambigous paths')
n_contracted = contract_edges(g, store_ordering=True)
print_stats(g)
logging.info('Saving scaffolding results')
save_fasta(g, '%s.fasta' % args.out)
save_ordering(g, '%s.ordering' % args.out)
def scaffold(args):
logging.info('Creating the scaffold graph')
g = load_from_fasta_tsv(args.fasta, args.edges, args.containment)
print_stats(g)
# delete small vertices
if args.min_ctg_len:
logging.info('Removing vertices smaller than %d bp' % args.min_ctg_len)
n_removed = 0
for v in g.vertices:
if len(v.seq) < args.min_ctg_len:
g.remove_vertex(v)
n_removed += 1
logging.info('Removed %d vertices' % n_removed)
print_stats(g)
# prune scaffold edges
if g.edges:
logging.info('Simplifying the graph using paired-end reads')
logging.info('Contracting unambigous paths')
contract_edges(g, store_ordering=True)
print_stats(g)
save_fasta(g, 'contracted.fasta')
if args.cut_tip_len:
n_cut = cut_tips(g, d=args.cut_tip_len)
logging.info('Cut %d tips shorter than %d bp' \
% (n_cut, args.cut_tip_len))
logging.info('Pruning edges with low support')
n_pruned1 = prune_scaffold_edges(g,
abs_support_thr=args.pe_abs_thr,
rel_support_thr=args.pe_rel_thr)
n_pruned2 = prune_scaffold_edges_via_wells(g, thr=args.pe_rc_rel_thr)
logging.info('%d edges pruned' % (n_pruned1 + n_pruned2))
logging.info('Contracting unambigous paths')
n_contracted = contract_edges(g)
print_stats(g)
# delete all existing edges from the graph
E = g.edges
for e in E:
g.remove_edge(e)
# create new edges whenever vertices have similar well profiles
logging.info('Creating edges from read clouds')
n_edges = make_wellscaff_edges(g,
min_common=args.rc_abs_thr,
min_thr=args.rc_rel_edge_thr)
logging.info('%d scaffold edges from read clouds' % n_edges)
logging.info('Auto-saving graph with prefix %s.wellscaff' % args.out)
save_to_fasta_tsv(g, '%s.wellscaff.fasta' % args.out,
'%s.wellscaff.tsv' % args.out,
'%s.wellscaff.containment' % args.out)
logging.info('Pruning edges with low support')
n_pruned = prune_via_wells(g,
min_common=args.rc_abs_thr,
min_thr=args.rc_rel_prun_thr)
logging.info('%d edges pruned' % n_pruned)
logging.info('Contracting unambigous paths')
n_contracted = contract_edges(g, store_ordering=True)
print_stats(g)
logging.info('Saving scaffolding results')
save_fasta(g, '%s.fasta' % args.out)
save_ordering(g, '%s.ordering' % args.out)
def scaffold_via_wells_mst(g):
# initialize internal contig labels (used for downstream qc)
for v in g.vertices:
v.initialize_contigs()
# construct well-based scaffold graph in networkx format
nxg = g.nxgraph
# nxg = _construct_graph(g)
# weigh edges according to how many wells they are sharing:
_reweigh_edges(nxg, g, type_='wells')
# find the maxinum spanning forest
msf = nx.minimum_spanning_tree(nxg)
# keep simplifying the graph until the msf has no branching nodes:
n_iter = 1
while _has_branches(msf) and n_iter <= 10:
print 'MSF simplificaiton iteration %d' % n_iter
# print '...', max(msf.degree(weight=None).values())
# print '...', sorted(msf.degree(weight=None).iteritems(), key=lambda x: x[1], reverse=True)[:10]
# vg = sorted(msf.degree(weight=None).iteritems(), key=lambda x: x[1], reverse=True)[0][0]
# v = g.vertex_from_id(vg[0])
# N = [n.id for n in g.vertices if v in n.neighbors]
# print ',,,', N
# print msf.neighbors(v)
# remove edges of g not selected in forest MSF
E = [e for e in g.edges]
n_removed = 0
for e in E:
e_nx = ((e.v1.id, e.connection[e.v1]), (e.v2.id,
e.connection[e.v2]))
if not msf.has_edge(*e_nx):
g.remove_edge(e)
n_removed += 1
print '%d edges not in MST removed.' % n_removed
# contract edges
n_contracted = contract_edges(g, store_ordering=True)
print '%d edges contracted.' % n_contracted
# now we are going to compute the trunk
# get the networkx graph again
nxg = g.nxgraph
_reweigh_edges(nxg, g, type_='wells') # FIXME: do this once
# recompute the maxinum spanning forest
msf = nx.minimum_spanning_tree(g.nxgraph)
# for each tree in forest:
trunk = list()
for mst in nx.connected_component_subgraphs(msf):
# add to mst trunk
if len(mst) >= 4:
trunk.extend(_mst_trunk(mst, g))
# remove edges not in trunk:
E = [e for e in g.edges]
print trunk
trunk_v = set([v[0] for v in trunk])
n_removed = 0
for e in E:
v1_id, v2_id = e.v1.id, e.v2.id
if v1_id not in trunk_v or v2_id not in trunk_v:
g.remove_edge(e)
n_removed += 1
if n_iter >= 4: keyboard()
print '%d edges not in trunk removed.' % n_removed
# contract one last time
n_contracted = contract_edges(g, store_ordering=True)
print '%d edges contracted.' % n_contracted
# construct well-based scaffold graph in networkx format
nxg = g.nxgraph
# nxg = _construct_graph(g)
# weigh edges according to how many wells they are sharing:
_reweigh_edges(nxg, g, type_='wells')
# find the maxinum spanning forest
msf = nx.minimum_spanning_tree(nxg)
n_iter += 1
def scaffold_via_wells_mst(g):
# initialize internal contig labels (used for downstream qc)
for v in g.vertices:
v.initialize_contigs()
# construct well-based scaffold graph in networkx format
nxg = g.nxgraph
# nxg = _construct_graph(g)
# weigh edges according to how many wells they are sharing:
_reweigh_edges(nxg, g, type_="wells")
# find the maxinum spanning forest
msf = nx.minimum_spanning_tree(nxg)
# keep simplifying the graph until the msf has no branching nodes:
n_iter = 1
while _has_branches(msf) and n_iter <= 10:
print "MSF simplificaiton iteration %d" % n_iter
# print '...', max(msf.degree(weight=None).values())
# print '...', sorted(msf.degree(weight=None).iteritems(), key=lambda x: x[1], reverse=True)[:10]
# vg = sorted(msf.degree(weight=None).iteritems(), key=lambda x: x[1], reverse=True)[0][0]
# v = g.vertex_from_id(vg[0])
# N = [n.id for n in g.vertices if v in n.neighbors]
# print ',,,', N
# print msf.neighbors(v)
# remove edges of g not selected in forest MSF
E = [e for e in g.edges]
n_removed = 0
for e in E:
e_nx = ((e.v1.id, e.connection[e.v1]), (e.v2.id, e.connection[e.v2]))
if not msf.has_edge(*e_nx):
g.remove_edge(e)
n_removed += 1
print "%d edges not in MST removed." % n_removed
# contract edges
n_contracted = contract_edges(g, store_ordering=True)
print "%d edges contracted." % n_contracted
# now we are going to compute the trunk
# get the networkx graph again
nxg = g.nxgraph
_reweigh_edges(nxg, g, type_="wells") # FIXME: do this once
# recompute the maxinum spanning forest
msf = nx.minimum_spanning_tree(g.nxgraph)
# for each tree in forest:
trunk = list()
for mst in nx.connected_component_subgraphs(msf):
# add to mst trunk
if len(mst) >= 4:
trunk.extend(_mst_trunk(mst, g))
# remove edges not in trunk:
E = [e for e in g.edges]
print trunk
trunk_v = set([v[0] for v in trunk])
n_removed = 0
for e in E:
v1_id, v2_id = e.v1.id, e.v2.id
if v1_id not in trunk_v or v2_id not in trunk_v:
g.remove_edge(e)
n_removed += 1
if n_iter >= 4:
keyboard()
print "%d edges not in trunk removed." % n_removed
# contract one last time
n_contracted = contract_edges(g, store_ordering=True)
print "%d edges contracted." % n_contracted
# construct well-based scaffold graph in networkx format
nxg = g.nxgraph
# nxg = _construct_graph(g)
# weigh edges according to how many wells they are sharing:
_reweigh_edges(nxg, g, type_="wells")
# find the maxinum spanning forest
msf = nx.minimum_spanning_tree(nxg)
n_iter += 1
