def main(argv=sys.argv):
G_asm = AsmGraph("sg_edges_list", "utg_data", "ctg_paths")
G_asm.load_sg_seq("preads4falcon.fasta")
utg_out = open("utgs.fa", "w")
for utg in G_asm.utg_data:
s, t, v = utg
type_, length, score, path_or_edges = G_asm.utg_data[(s, t, v)]
if type_ == "simple":
path_or_edges = path_or_edges.split("~")
seq = G_asm.get_seq_from_path(path_or_edges)
print >> utg_out, ">%s~%s~%s-%d %d %d" % (s, v, t, 0, length,
score)
print >> utg_out, seq
if type_ == "compound":
c_graph = nx.DiGraph()
all_alt_path = []
path_or_edges = [c.split("~") for c in path_or_edges.split("|")]
for ss, vv, tt in path_or_edges:
type_, length, score, sub_path = G_asm.utg_data[(ss, tt, vv)]
sub_path = sub_path.split("~")
v1 = sub_path[0]
for v2 in sub_path[1:]:
c_graph.add_edge(v1,
v2,
e_score=G_asm.sg_edges[(v1, v2)][1])
v1 = v2
shortest_path = nx.shortest_path(c_graph, s, t, "e_score")
score = nx.shortest_path_length(c_graph, s, t, "e_score")
all_alt_path.append((score, shortest_path))
# a_ctg_data.append( (s, t, shortest_path) ) #first path is the same as the one used in the primary contig
while 1:
if s == t:
break
n0 = shortest_path[0]
for n1 in shortest_path[1:]:
c_graph.remove_edge(n0, n1)
n0 = n1
try:
shortest_path = nx.shortest_path(c_graph, s, t, "e_score")
score = nx.shortest_path_length(c_graph, s, t, "e_score")
#a_ctg_data.append( (s, t, shortest_path) )
all_alt_path.append((score, shortest_path))
except nx.exception.NetworkXNoPath:
break
# if len(shortest_path) < 2:
# break
all_alt_path.sort()
all_alt_path.reverse()
shortest_path = all_alt_path[0][1]
score, atig_path = all_alt_path[0]
atig_output = []
atig_path_edges = zip(atig_path[:-1], atig_path[1:])
sub_seqs = []
total_length = 0
total_score = 0
for vv, ww in atig_path_edges:
r, aln_score, idt, typs_ = G_asm.sg_edges[(vv, ww)]
e_seq = G_asm.sg_edge_seqs[(vv, ww)]
rid, ss, tt = r
sub_seqs.append(e_seq)
total_length += abs(ss - tt)
total_score += aln_score
base_seq = "".join(sub_seqs)
atig_output.append((s, t, atig_path, total_length, total_score,
base_seq, atig_path_edges, 1, 1))
duplicated = True
for score, atig_path in all_alt_path[1:]:
atig_path_edges = zip(atig_path[:-1], atig_path[1:])
sub_seqs = []
total_length = 0
total_score = 0
for vv, ww in atig_path_edges:
r, aln_score, idt, type_ = G_asm.sg_edges[(vv, ww)]
e_seq = G_asm.sg_edge_seqs[(vv, ww)]
rid, ss, tt = r
sub_seqs.append(e_seq)
total_length += abs(ss - tt)
total_score += aln_score
seq = "".join(sub_seqs)
aln_data, x, y = get_aln_data(base_seq, seq)
if len(aln_data) != 0:
idt = 1.0 - 1.0 * aln_data[-1][-1] / aln_data[-1][-2]
cov = 1.0 * (aln_data[-1][3] -
aln_data[-1][2]) / aln_data[-1][4]
if idt < 0.96 or cov < 0.98:
duplicated = False
atig_output.append(
(s, t, atig_path, total_length, total_score, seq,
atig_path_edges, idt, cov))
else:
duplicated = False
atig_output.append(
(s, t, atig_path, total_length, total_score, seq,
atig_path_edges, 0, 0))
# if len(atig_output) == 1:
# continue
sub_id = 0
for data in atig_output:
v0, w0, tig_path, total_length, total_score, seq, atig_path_edges, a_idt, cov = data
print >> utg_out, ">%s~%s~%s-%d %d %d" % (
v0, "NA", w0, sub_id, total_length, total_score)
print >> utg_out, seq
sub_id += 1
def main(argv=None):
G_asm = AsmGraph("sg_edges_list", "utg_data", "ctg_paths")
G_asm.load_sg_seq("preads4falcon.fasta")
utg_out = open("utgs.fa","w")
for utg in G_asm.utg_data:
s,t,v = utg
type_, length, score, path_or_edges = G_asm.utg_data[ (s,t,v) ]
if type_ == "simple":
path_or_edges = path_or_edges.split("~")
seq = G_asm.get_seq_from_path( path_or_edges )
print >> utg_out, ">%s~%s~%s-%d %d %d" % (s, v, t, 0, length, score )
print >> utg_out, seq
if type_ == "compound":
c_graph = nx.DiGraph()
all_alt_path = []
path_or_edges = [ c.split("~") for c in path_or_edges.split("|")]
for ss, vv, tt in path_or_edges:
type_, length, score, sub_path = G_asm.utg_data[ (ss,tt,vv) ]
sub_path = sub_path.split("~")
v1 = sub_path[0]
for v2 in sub_path[1:]:
c_graph.add_edge( v1, v2, e_score = G_asm.sg_edges[ (v1, v2) ][1] )
v1 = v2
shortest_path = nx.shortest_path( c_graph, s, t, "e_score" )
score = nx.shortest_path_length( c_graph, s, t, "e_score" )
all_alt_path.append( (score, shortest_path) )
#a_ctg_data.append( (s, t, shortest_path) ) #first path is the same as the one used in the primary contig
while 1:
if s == t:
break
n0 = shortest_path[0]
for n1 in shortest_path[1:]:
c_graph.remove_edge(n0, n1)
n0 = n1
try:
shortest_path = nx.shortest_path( c_graph, s, t, "e_score" )
score = nx.shortest_path_length( c_graph, s, t, "e_score" )
#a_ctg_data.append( (s, t, shortest_path) )
all_alt_path.append( (score, shortest_path) )
except nx.exception.NetworkXNoPath:
break
#if len(shortest_path) < 2:
# break
all_alt_path.sort()
all_alt_path.reverse()
shortest_path = all_alt_path[0][1]
score, atig_path = all_alt_path[0]
atig_output = []
atig_path_edges = zip(atig_path[:-1], atig_path[1:])
sub_seqs = []
total_length = 0
total_score = 0
for vv, ww in atig_path_edges:
r, aln_score, idt, typs_ = G_asm.sg_edges[ (vv, ww) ]
e_seq = G_asm.sg_edge_seqs[ (vv, ww) ]
rid, ss, tt = r
sub_seqs.append( e_seq )
total_length += abs(ss-tt)
total_score += aln_score
base_seq = "".join(sub_seqs)
atig_output.append( (s, t, atig_path, total_length, total_score, base_seq, atig_path_edges, 1, 1) )
duplicated = True
for score, atig_path in all_alt_path[1:]:
atig_path_edges = zip(atig_path[:-1], atig_path[1:])
sub_seqs = []
total_length = 0
total_score = 0
for vv, ww in atig_path_edges:
r, aln_score, idt, type_ = G_asm.sg_edges[ (vv, ww) ]
e_seq = G_asm.sg_edge_seqs[ (vv, ww) ]
rid, ss, tt = r
sub_seqs.append( e_seq )
total_length += abs(ss-tt)
total_score += aln_score
seq = "".join(sub_seqs)
aln_data, x, y = get_aln_data(base_seq, seq)
if len( aln_data ) != 0:
idt = 1.0-1.0*aln_data[-1][-1] / aln_data[-1][-2]
cov = 1.0*(aln_data[-1][3]-aln_data[-1][2])/aln_data[-1][4]
if idt < 0.96 or cov < 0.98:
duplicated = False
atig_output.append( (s, t, atig_path, total_length, total_score, seq, atig_path_edges, idt, cov) )
else:
duplicated = False
atig_output.append( (s, t, atig_path, total_length, total_score, seq, atig_path_edges, 0, 0) )
#if len(atig_output) == 1:
# continue
sub_id = 0
for data in atig_output:
v0, w0, tig_path, total_length, total_score, seq, atig_path_edges, a_idt, cov = data
print >> utg_out, ">%s~%s~%s-%d %d %d" % (v0, "NA", w0, sub_id, total_length, total_score )
print >> utg_out, seq
sub_id += 1
if alignment[0].aln_str_size > 100:
aln_data.append((q_id, 0, s1, e1, len(q_seq), s2, e2, len(seq0),
alignment[0].aln_str_size, alignment[0].dist))
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data, x, y
G_asm = AsmGraph("sg_edges_list", "utg_data", "ctg_paths")
G_asm.load_sg_seq("preads4falcon.fasta")
utg_out = open("utgs.fa", "w")
for utg in G_asm.utg_data:
s, t, v = utg
type_, length, score, path_or_edges = G_asm.utg_data[(s, t, v)]
if type_ == "simple":
path_or_edges = path_or_edges.split("~")
seq = G_asm.get_seq_from_path(path_or_edges)
print >> utg_out, ">%s~%s~%s-%d %d %d" % (s, v, t, 0, length, score)
print >> utg_out, seq
if type_ == "compound":
c_graph = nx.DiGraph()
aln_data.append(
(q_id, 0, s1, e1, len(q_seq), s2, e2, len(seq0), alignment[0].aln_str_size, alignment[0].dist)
)
aln_str1 = alignment[0].q_aln_str
aln_str0 = alignment[0].t_aln_str
DWA.free_alignment(alignment)
kup.free_kmer_lookup(lk_ptr)
kup.free_seq_array(sa_ptr)
kup.free_seq_addr_array(sda_ptr)
return aln_data, x, y
G_asm = AsmGraph("sg_edges_list", "utg_data", "ctg_paths")
G_asm.load_sg_seq("preads4falcon.fasta")
utg_out = open("utgs.fa", "w")
for utg in G_asm.utg_data:
s, t, v = utg
type_, length, score, path_or_edges = G_asm.utg_data[(s, t, v)]
if type_ == "simple":
path_or_edges = path_or_edges.split("~")
seq = G_asm.get_seq_from_path(path_or_edges)
print >> utg_out, ">%s~%s~%s-%d %d %d" % (s, v, t, 0, length, score)
print >> utg_out, seq
if type_ == "compound":
