used.append(node)
next = getStrongestEdge(node, direction, used)
if next is None:
break
path.append(next)
if next.qstrand == '-':
if direction == SUPPORTFLAGS.left:
direction = SUPPORTFLAGS.right
elif direction == SUPPORTFLAGS.right:
direction = SUPPORTFLAGS.left
node = next.qname
paths.append(path)
for p in paths:
if len(p) == 0:
continue
for i in p:
if not i.tname.startswith("ref"):
sys.stdout.write(i.tname.split('/')[1], i.tstrand, "\t")
else:
sys.stdout.write(i.tname, i.tstrand, "\t")
sys.stdout.write('\n')
if __name__ == '__main__':
reads = sys.argv[1]
fasta = FastaFile(reads)
#blasr(reads, reads, 4)
ovl = m5ToOvlGraph(fasta.keys(), "out.m5")
ovlSimplify(ovl)
nx.write_gml(ovl, "ovl.gml")
import sys, random
from pbsuite.utils.FileHandlers import FastaFile, revComp, wrap
def getRandomSeq(length):
return "".join([random.choice(['A', 'T', 'C', 'G']) for i in xrange(length)])
if __name__ == '__main__':
fasta = FastaFile(sys.argv[1])
key = fasta.keys()[0]
ref = list(fasta[key])
#800bp insertion in the sample (deletion in the reference)
ref[5000:5800] = ""
#5000 Insertion
#Inversion in the sample (inversion in the reference) tails
ref[9000:12000] = list("".join(ref[10000:13000]).translate(revComp)[::-1])
#9000-12000 - INversion
#1kb deletion in sample (insert into the reference) tails
seq = getRandomSeq(1000)
ref[20000:20000] = list(seq)
#20000-21000 -- Deletion
#100bp insertion in sample (deletion in the reference) spots
ref[30000:30100] = ""
#30000 - Insertion
#200bp deletion in sample (insert into the reference) spots
seq = getRandomSeq(200)
ref[35000:35000] = list(seq)