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#!/usr/bin/env python
from __future__ import division
import sys
import os
import argparse
import string
from collections import Counter
import random
sys.path.append(os.path.dirname(__file__));
import readSeq
import multiprocessing
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
KMER = 16
SUBLEN = 1000000
def getArgs():
parser = argparse.ArgumentParser(description="Count occurance of database kmers in reads", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-k', default=KMER, dest='kmer', metavar='<int>', type=int, help="kmer length")
parser.add_argument('-l', dest='sublen', metavar='<int>', type=int, help="perform analysis on first <int> bases [RDLEN - K + 1]")
parser.add_argument('-c', default=2, dest='cutoff', metavar='<int>', type=int, help="minimum allowed coverage")
parser.add_argument('-t', default=30, dest='targetCov', metavar='<int>', type=int, help="target coverage")
parser.add_argument('-p', '--plot', dest='plot', type=str, default=None, metavar="<file>", help='plot data and save as png to <file>')
parser.add_argument('fastaFile', type=str, help='Input FASTA file(s). Text or gzip')
parser.add_argument('fastqFile', nargs='+', help='Input FASTQ file(s). Text or gzip')
args = parser.parse_args()
return args
def getMers(seq, merLen):
for i in xrange(min(len(seq) - merLen + 1,SUBLEN)):
yield seq[i:i+merLen]
complements = string.maketrans('acgtACGT', 'tgcaTGCA')
def revComp(seq):
revCompSeq = seq.translate(complements)[::-1]
return revCompSeq
def tallyPositions(seq,counts,sublen=None):
readPos = 0
for mer in getMers(seq, KMER):
if mer in merCnts:
if readPos > len(counts):
counts.append(1)
else:
counts[readPos] += 1
readPos += 1
if sublen:
if readPos == sublen:
break
#end tallyPositions
def main():
"""
kmer based normization
call rand once
004
if avecov1|2 < mincov:
trash
elif avecov1|2 < target:
keep
elif random < target/avecov1|2:
keep
else:
trash
"""
args = getArgs()
global KMER
KMER = args.kmer
out=sys.stdout
#check to make sure input files exist
for fq in args.fastqFile:
if not os.path.exists(fq):
sys.stderr.write("ERROR: Input file '%s' does not exist. Exiting.\n" % fq)
sys.exit()
#count mers / create database
sys.stderr.write("Making k-mer database\n")
global merCnts
merCnts = Counter()
for record in readSeq.readSeq(args.fastaFile,fileType='fasta'):
for mer in getMers(record.seq, args.kmer):
sortMers = sorted([mer, revComp(mer)])
merCnts[mer] += 1
merCnts[revComp(mer)] += 1
#normalize reads
sys.stderr.write("Tallying occurrences of database kmers in reads\n")
seqIt = readSeq.readSeq(fq,paired=True)
record1,record2 = seqIt.next()
readLen = len(record1.seq)
sys.stderr.write("Read length = %d\n" % readLen)
tallyLen = readLen - args.kmer + 1
if args.sublen:
if args.sublen > tallyLen:
sys.stderr.write("sublen (-l) must be less than readlen - k + 1 : (found reads of length %d\n" % readLen)
sys.exit(-1)
tallyLen = args.sublen
counts1 = [0 for x in range(tallyLen)]
counts2 = [0 for x in range(tallyLen)]
tallyPositions(record1.seq,counts1,tallyLen)
tallyPositions(record2.seq,counts2,tallyLen)
total_reads = 1
fqName = ""
for fq in args.fastqFile:
for record1, record2 in seqIt:
tallyPositions(record1.seq,counts1,tallyLen)
tallyPositions(record2.seq,counts2,tallyLen)
total_reads += 1
fqName += fq+" "
counts1_perc = [ 100 * float(x)/total_reads for x in counts1 ]
counts2_perc = [ 100 * float(x)/total_reads for x in counts2 ]
out.write("#pos\tread1_count\tread1_perc\tread2_count\tread2_perc\n")
for i in range(tallyLen):
out.write("%i\t%i\t%0.2f\t%i\t%0.2f\n" % (i+1,counts1[i],counts1_perc[i],counts2[i],counts2_perc[i]))
if args.plot:
sys.stderr.write("Plotting data. Saving to %s\n" % args.plot)
plt.ioff()
xcoord = range(1,tallyLen+1)
plt.plot(xcoord,counts1_perc,color="red",linewidth=1.0,linestyle="-",label="Read 1")
plt.plot(xcoord,counts2_perc,color="green",linewidth=1.0,linestyle="-",label="Read 2")
leg_loc="upper right"
max_cnt = 0
max_pos = 0
for i in range(len(counts1)):
if counts1[i] > max_cnt or counts2[i] > max_cnt:
max_cnt = counts1[i] if counts1[i] > counts2[i] else counts2[i]
max_pos = i
if max_pos > 0.5*len(counts1) :
leg_loc="upper left"
plt.legend(loc=leg_loc,prop={'size':10})
plt.xlabel("Read Position")
plt.ylabel("Percent Reads with Database k-mer")
plt.title("Occurrence of reference k-mers (k = %i) in \n%s (# reads = %d)" % (args.kmer,fqName,total_reads))
plt.savefig(args.plot)
if __name__ == '__main__':
try:
main()
except KeyboardInterrupt:
pass
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