def main(reads_file, ref_file, dir, error_rate):
sys.stderr.write("Reading reference" + "\n")
ref = sorted(list(SeqIO.parse_fasta(open(ref_file, "r"))),
key=lambda rec: len(rec))[-1]
ref = Contig(ref.seq, ref.id)
refs = ContigCollection()
for i in range(0, len(ref) - 500, 500):
if random.random() > 0.95:
tmp = list(ref.segment(i, i + 500).Seq())
for j in range(error_rate * 500 / 100):
pos = random.randint(0, 499)
tmp[pos] = basic.rc[tmp[pos]]
refs.add(
Contig("".join(tmp),
ref.id + "(" + str(i) + "," + str(i + 500) + ")"))
refs.print_names(sys.stderr)
sys.stderr.write("Reading reads" + "\n")
reads = ReadCollection()
reads.loadFromFasta(open(reads_file, "r"))
sys.stderr.write("Aligning reads" + "\n")
basic.ensure_dir_existance(dir)
aligner = Aligner(DirDistributor(dir))
aligner.alignReadCollection(reads, refs)
sys.stderr.write("Analysing alignments" + "\n")
alignments = []
for read in reads:
alignments.extend(read.alignments)
alignments = filter(lambda al: len(al) > 450, alignments)
alignments = sorted(alignments,
key=lambda al:
(al.seg_to.contig.id, al.seg_from.contig.id))
scorer = Scorer()
scorer.scores.homo_score = 3
scorer.scores.ins_score = 5
scorer.scores.del_score = 5
cnt = 0
for contig, iter in itertools.groupby(alignments,
key=lambda al: al.seg_to.contig):
iter = list(iter)
sys.stderr.write(str(contig) + " " + str(len(iter)) + "\n")
if len(iter) < 150:
for al in iter:
print scorer.accurateScore(al.matchingSequence(),
params.alignment_correction_radius)
cnt += 1
if cnt >= 5000:
break
if cnt >= 5000:
break
def main(contigs_file, contig_name, reads_file, dir, k, initial_reads1, initial_reads2):
basic.ensure_dir_existance(dir)
basic.CreateLog(dir)
dd = DirDistributor(os.path.join(dir, "alignments"))
aligner = Aligner(dd)
contigs = ContigStorage().loadFromFasta(open(contigs_file, "r"), False)
# contig = contigs[contig_name].asSegment().prefix(length=2000).asContig()
contig = contigs[contig_name]
reads = ContigStorage().loadFromFasta(open(reads_file, "r"), False)
reads1 = ContigStorage()
reads2 = ContigStorage()
cnt = 0
for read in reads.unique():
cnt += 1
# if cnt % 2 == 0:
if read.id in initial_reads1:
reads1.add(read)
elif read.id in initial_reads2:
reads2.add(read)
polisher = Polisher(aligner, dd)
contig1 = contig
contig2 = contig
scorer = Scorer()
for i in range(3):
diff = 0
print "Iteration", i
als1 = fixAlDir(aligner.overlapAlign(reads1.unique(), ContigStorage([contig])), contig)
als2 = fixAlDir(aligner.overlapAlign(reads2.unique(), ContigStorage([contig])), contig)
contig1 = Contig(polisher.polishSmallSegment(contig.asSegment(), als1).seg_from.Seq(), "1")
contig2 = Contig(polisher.polishSmallSegment(contig.asSegment(), als2).seg_from.Seq(), "2")
al = aligner.overlapAlign([contig1], ContigStorage([contig2])).next()
als1 = fixAlDir(aligner.overlapAlign(reads.unique(), ContigStorage([contig1])), contig1)
als1 = filter(lambda al: len(al.seg_to) > len(al.seg_to.contig) - 100, als1)
als2 = fixAlDir(aligner.overlapAlign(reads.unique(), ContigStorage([contig2])), contig2)
als2 = filter(lambda al: len(al.seg_to) > len(al.seg_to.contig) - 100, als2)
als1 = sorted(als1, key = lambda al: al.seg_from.contig.id)
als2 = sorted(als2, key = lambda al: al.seg_from.contig.id)
reads1 = ContigStorage()
reads2 = ContigStorage()
dp = scorer.accurateScore(al.matchingSequence(), 10) #1 - al.percentIdentity()
als_map = dict()
for al in als1:
als_map[al.seg_from.contig.id] = [al]
for al in als2:
if al.seg_from.contig.id in als_map:
als_map[al.seg_from.contig.id].append(al)
com_res = []
diffs = []
for tmp_als in als_map.values():
if len(tmp_als) != 2:
continue
al1 = tmp_als[0]
al2 = tmp_als[1]
print al1, al2
assert al1.seg_from.contig == al2.seg_from.contig
pi1 = scorer.accurateScore(al1.matchingSequence(), 10) # al1.percentIdentity()
pi2 = scorer.accurateScore(al2.matchingSequence(), 10) # al2.percentIdentity()
com_res.append((al1, al2, pi1 - pi2))
diffs.append(pi1 - pi2)
diffs = sorted(diffs)
th1 = diffs[len(diffs) / 4]
th2 = diffs[len(diffs) * 3 / 4]
print "Thresholds:", th1, th2
for al1, al2, diff in com_res:
if diff < th1:
reads1.add(al1.seg_from.contig)
elif diff > th2:
reads2.add(al2.seg_from.contig)
# if pi1 > pi2 + dp / 4:
# reads1.add(al1.seg_from.contig)
# elif pi2 > pi1 + dp / 4:
# reads2.add(al2.seg_from.contig)
# diff += abs(pi1 - pi2)
print float(diff) / len(als1), len(reads1) / 2, len(reads2) / 2
al = aligner.overlapAlign([contig1], ContigStorage([contig2])).next()
print al
print "\n".join(al.asMatchingStrings2())
for read in reads1:
if read.id in initial_reads1:
sys.stdout.write(read.id + " ")
print ""
for read in reads2:
if read.id in initial_reads2:
sys.stdout.write(read.id + " ")
print ""
contig1 = prolong(aligner, polisher, contig1, reads1)
contig2 = prolong(aligner, polisher, contig2, reads2)
contig1.id = "1"
contig2.id = "2"
out = open(os.path.join(dir, "copies.fasta"), "w")
SeqIO.write(contig1, out, "fasta")
SeqIO.write(contig2, out, "fasta")
out.close()
out = open(os.path.join(dir, "reads1.fasta"), "w")
for read in reads1.unique():
SeqIO.write(read, out, "fasta")
out.close()
out = open(os.path.join(dir, "reads2.fasta"), "w")
for read in reads2.unique():
SeqIO.write(read, out, "fasta")
out.close()
print "Finished"