def view(args):
g = load_from_fasta_tsv(args.fasta, args.edges, args.containment)
# save_to_fasta_tsv(g, 'test.fasta', 'test.tsv', 'test.containment')
# g = load_from_fasta_tsv('test.fasta', 'test.tsv', 'test.containment')
if args.check_correctness:
visualize_correctness(g)
if args.vertex:
print_vertex(g.vertex_from_id(args.vertex))
if args.edge:
print_connection(g.get_edge(args.edge))
if args.dot:
to_graphviz_dot(g, args.dot)
if args.gfa:
save_bandage_gfa(g, args.gfa)
def view(args):
g = load_from_fasta_tsv(args.fasta, args.edges, args.containment)
# save_to_fasta_tsv(g, 'test.fasta', 'test.tsv', 'test.containment')
# g = load_from_fasta_tsv('test.fasta', 'test.tsv', 'test.containment')
if args.check_correctness:
visualize_correctness(g)
if args.vertex:
print_vertex(g.vertex_from_id(args.vertex))
if args.edge:
print_connection(g.get_edge(args.edge))
if args.dot:
to_graphviz_dot(g, args.dot)
if args.gfa:
save_bandage_gfa(g, args.gfa)
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)
