def PrintResults(recs, reference, references_file, coordinates_file):
aln = open(coordinates_file, "w")
fasta = open(references_file, "w")
for rec in recs:
aln.write(str(rec) + "\n")
sequence = reference[rec.rname][rec.left:rec.right]
rec_id = str(rec.rname) + "_(" + str(rec.left) + "-" + str(rec.right)+")"
SeqIO.write(SeqIO.SeqRecord(sequence, rec_id), fasta, "fasta")
aln.close()
fasta.close()
def main(argv):
sys.stdout.write("Started\n")
dot_file = argv[1]
edge_sequences = argv[2]
reference_file = argv[3]
alignment_file = argv[4]
edges = ParseVertices(argv[5])
output_file = argv[6]
sys.stdout.write("Loading dot\n")
dot = DotParser(open(dot_file, "r")).parse()
edge_collection = ContigCollection().loadFromFasta(
open(edge_sequences, "r"), True)
graph = Graph().loadFromDot(edge_collection, dot)
vertices = [graph.E[id].start.id for id in edges]
graph.printToFile(sys.stdout)
print vertices
ref = ContigCollection().loadFromFasta(open(reference_file, "r"), False)
print "Looking for relevant"
pq = PriorityQueue()
for v in graph.V.values():
if v.id in vertices:
pq.push((0, v))
visited = []
while not pq.empty():
d, v = pq.pop()
if v in visited:
continue
visited.append(v)
for e in v.inc:
print e.id, e.start.id, e.end.id
if d + len(e) < dist:
pq.push((d + len(e), e.start))
for e in v.out:
print e.id, e.start.id, e.end.id
if d + len(e) < dist:
pq.push((d + len(e), e.end))
print "Visited", len(visited)
print map(str, list(visited))
relevant = []
edge_alignments = ReadCollection().loadFromFasta(open(edge_sequences,
"r")).addAllRC()
for edge in graph.E.values():
if edge.start in visited or edge.start.rc in visited:
relevant.append(edge_alignments[edge.id])
print "Loading sam"
edge_alignments.fillFromSam(Samfile(open(alignment_file, "r")), ref)
for rel in relevant:
print rel.__str__()
print "Collecting segments"
segments = []
chr1 = ref["chr1"]
for edge in relevant:
for al in edge.alignments:
print al
if al.seg_from.inter(edge.prefix(dist)):
l = dist - al.seg_from.left
contig = al.seg_to.contig
start = al.seg_to.left
segments.append(
Segment(contig, start, min(start + l, len(contig))))
print segments[-1]
tmp = []
print "Rotating"
for seg in segments:
if seg.contig != chr1:
seg = seg.RC()
if seg.contig != chr1:
print "WARNING", seg
tmp.append(seg)
segments = sorted(tmp, key=lambda seg: seg.left)
print "All relevant segments"
print "\n".join(map(str, segments))
cur_seg = None
interesting_segments = []
print "Gluing"
for seg in segments:
if cur_seg is None:
cur_seg = seg.copy()
continue
if cur_seg.right + 20000 < seg.left:
interesting_segments.append(cur_seg.copy())
cur_seg = seg.copy()
else:
cur_seg.right = max(cur_seg.right, seg.right)
if cur_seg is not None:
interesting_segments.append(cur_seg.copy())
alignments = []
for edge in edge_alignments:
for al in edge.alignments:
ok = False
for seg in interesting_segments:
if al.seg_to.inter(seg):
alignments.append(al)
alignments = sorted(alignments, key=lambda al: al.seg_to.left)
print "All relevant alignments"
print "\n".join(map(str, alignments))
print "Interesting segments:", len(interesting_segments), sum(
map(len, interesting_segments))
for seg in interesting_segments:
print seg
f = open(output_file, "w")
tmp = []
for seg in interesting_segments:
SeqIO.write(SeqIO.SeqRecord(seg.Seq(), seg.__str__()), f, "fasta")
tmp.append(seg.Seq())
f.close()
f1 = open(output_file + "1", "w")
SeqIO.write(SeqIO.SeqRecord(("N" * 20000).join(tmp), "concat"), f1,
"fasta")