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#!/usr/bin/python
import sys, re, random, argparse, textwrap, logging
import operator
from collections import defaultdict, namedtuple
from pbsuite.utils.FileHandlers import FastaFile, M5File, FastqFile
from pbsuite.utils.CommandRunner import exe
from pbsuite.utils.setupLogging import setupLogging
USAGE = """\
Takes reads.fastq and ref.fasta
maps with blasr
creates consensus
"""
def blasr(query, target, nproc=1, bestn=1, outName="map.m5"):
"""
runs blasr
"""
r,o,e = exe("blasr %s %s --bestn %d --affineAlign -m 5 --nproc %d --out %s" \
% (query, target, bestn, nproc, outName))
def realign(alignment):
"""
realigns target, query so that every alignment should
have the comparable characteristics in the same sequence context
regardless of differences due to the error rate and alignment
variation
realignment happens inplace
"""
def inner(align):
target = list(align.targetSeq)
query = list(align.querySeq)
compSeq = list(align.compSeq)
for pos in range(len(align.targetSeq)):
if align.targetSeq[pos] == '-':
i = re.match('-+[ATCGatcg]?', align.targetSeq[pos:])
if align.targetSeq[pos+i.end()-1] == align.querySeq[pos]:
target[pos] = align.targetSeq[pos+i.end()-1]
compSeq[pos] = '|'
target[pos+i.end()-1] = '-'
compSeq[pos+i.end()-1] = '*'
align.targetSeq = "".join(target)
align.compSeq = "".join(compSeq)
inner(alignment)
alignment.targetSeq, alignment.querySeq = alignment.querySeq, alignment.targetSeq
inner(alignment)
alignment.targetSeq, alignment.querySeq = alignment.querySeq, alignment.targetSeq
def offSetSeqs(offset, align):
q = [" "]*offset; q.extend(list(align.querySeq))
c = [" "]*offset; c.extend(list(align.compSeq))
t = [" "]*offset; t.extend(list(align.targetSeq))
return q,c,t
def printSeqs(seqs):
for s in seqs:
q,c,t = s
logging.debug( "".join(q))
logging.debug( "".join(c))
logging.debug( "".join(t))
def insert(base, pos, ch):
base[0].insert(pos, ch)
base[1].insert(pos, ch)
base[2].insert(pos, ch)
def consensus(aligns):
"""
expands alignment based on query, and then majority rules consensus the seqs
"""
if len(aligns) > 500:#hard limit
keep = []
scores = map(lambda x: x.score, aligns)
scores.sort()
minS = scores[499]
aligns = filter(lambda x: x.score <= minS, aligns)
seqs = []
for i in aligns:
realign(i)
seqs.append(offSetSeqs(i.tstart, i))
#logging.debug("#Original Seqs (%d)" % (len(seqs)))
#printSeqs(seqs)
i = 0 #<-- target relative position
remain = len(seqs) # number of sequences remaining
while remain > 1:
ins = False # Is there an insertion here
for base in seqs:
if i == len(base[1]):
remain -= 1# kill it
if i < len(base[1]) and base[2][i] == '-':
ins = True
if ins: # apply insertion across all non-ins bases
for base in seqs:
if i < len(base[1]):
if base[2][i] != '-' and base[2][i] != " ":
insert(base, i ,'_')
elif base[2][i] == " ":
insert(base, i, ' ')
i += 1
#logging.debug( "#Expanded Seqs" )
#printSeqs(seqs)
#majority vote consensus
out = []
contribBases = 0
fillBases = 0
if len(seqs) == 0:
logging.info("no sequences")
for p in range(max(map(lambda x: len(x[0]), seqs))):
cnt = defaultdict(int)
#Count it
for s in seqs:
if p < len(s[0]):
cnt[s[0][p]] += 1
cnt[" "] = 0
contribBases += sum(cnt.values())
#Maximum count
nuc = max(cnt.iteritems(), key=operator.itemgetter(1))[1]
#Who all has maximum count
n = []
for j in cnt:
if cnt[j] == nuc:
n.append(j)
#get random one
n = random.sample(n, 1)[0]
if n not in ["-","_"]:
fillBases += 1
out.append(n)
consen = "".join(out)
logging.debug("# expanded consensus (%d nuc votes) <%d fill bases>" % (contribBases, fillBases))
#logging.debug(consen)
consen = consen.replace('_','').replace('-','').replace(' ','')
results = namedtuple("polish_results", "contribSeqs contribBases fillBases sequence")
return results(len(aligns), contribBases, fillBases, consen)
def parseArgs():
parser = argparse.ArgumentParser(description=USAGE, \
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument("reads", metavar="reads", type=str, \
help="Input reads .fasta or .fastq")
parser.add_argument("-t", "--target", type=str, \
help="Target sequence name")
parser.add_argument("-T", "--Target", type=str, \
help="Fasta file containing target sequence")
parser.add_argument("-s", "--super", dest="super", action="store_true",\
help="Treat each read as the target once")
parser.add_argument("-m", "--maxtail", type = int, default=sys.maxint, \
help="Max number of bases allowed to be in tail (inf)")
parser.add_argument("-n", "--nproc", dest="nproc", default=1, type=int,\
help="Number of processors to use with blasr (1)")
parser.add_argument("-o", "--outname", dest="outname", default="polish.out", \
type=str, \
help="Base name for output files (polish.out)")
parser.add_argument("--debug", action="store_true")
args = parser.parse_args()
setupLogging(args.debug)
#I don't think this is exhaustive
if (args.target is not None and args.Target is not None) \
or (args.super and (args.target is not None or args.Target is not None)):
print "Error! only specify one of --super or --target or --Target"
exit(1)
return args
class NullDevice():
def write(self, s):
pass
if __name__ == '__main__':
args = parseArgs()
alignFile = args.outname+".m5"
consensusFile = args.outname+".fasta"
#extract the read I'm looking for
if args.target is not None:#Name
tempOut = open("temp.fasta",'w')
fasta = FastaFile(args.reads)
tempOut.write(">%s\n%s\n" % (args.target, fasta[args.target]))
tempOut.write
blasr(args.reads, tempOut.name, nproc=args.nproc, outName=alignFile)
aligns = M5File(alignFile)
fout = open(consensusFile, 'w')
results = consensus(aligns)
fout.write(">pbjpolish_%d_vote_%d_len\n" % (results.contribBases,\
results.fillBases, results.sequence))
#fout.write(">\n%s\n" % consensus(aligns))
fout.close()
elif args.Target is not None:#File
blasr(args.reads, args.Target, nproc=args.nproc, outName=alignFile)
aligns = M5File(alignFile)
fout = open(consensusFile, 'w')
results = consensus(aligns)
fout.write(">pbjpolish_%d_vote_%d_len\n%s\n" % (results.contribBases,\
results.fillBases, results.sequence))
#fout.write(">%s\n%s\n" % consensus(aligns))
fout.close()
elif args.super:#All
tempfile = open("temp.fasta",'w')
if args.reads.endswith(".fasta"):
seqs = FastaFile(args.reads)
#temp flie
for s in seqs:
tempfile.write(">%s\n%s\n" % (s, seqs[s]))
elif args.reads.endswith(".fastq"):
seqs = FastqFile(args.reads)
#temp file
for s in seqs:
tempfile.write(">%s\n%s\n" % (s, seqs[s].seq))
blasr(args.reads, tempfile.name, nproc=args.nproc, bestn=len(seqs), outName=alignFile)
aligns = M5File(alignFile)
groups = defaultdict(list)
for a in aligns:
groups[a.tname].append(a)
fout = open(consensusFile, 'w')
for g in groups:
results = consensus(aligns)
fout.write(">pbjpolish_%d_vote_%d_len\n" % (results.contribBases,\
results.fillBases, results.sequence))
fout.close()
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