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import random
import argparse
import os
import sys
import time
def find_out_length(infiles,amount,file_type):
infile1 = open(infiles[0])
lengths1 = []
lengths2 = []
i = 0
if file_type == "fastq":
name = infile1.readline()
while i <= amount+1 and name != "":
lengths1.append(len(infile1.readline())-1)
infile1.readline()
infile1.readline()
name = infile1.readline()
i += 1
if file_type == "fasta":
while i <= amount+1 and name != "":
lengths1.append(len(infile1.readline())-1)
name = infile1.readline()
i += 1
if not SingleEnd:
infile2 = open(infiles[1])
i = 0
name = infile2.readline()
if file_type == "fastq":
while i <= amount+1 and name != "":
lengths2.append(len(infile2.readline())-1)
infile2.readline()
infile2.readline()
name = infile2.readline()
i += 1
if file_type == "fasta":
while i <= amount+1 and name != "":
lengths2.append(len(infile2.readline())-1)
name = infile2.readline()
i += 1
infile2.close()
else:
lengths2 = [0]*len(lengths1)
infile1.close()
j = 0
while len(lengths1) <= amount:
lengths1.append(lengths1[j])
j += 1
j = 0
while len(lengths2) <= amount:
lengths2.append(lengths2[j])
j += 1
return lengths1,lengths2
def checkread(read,verbose,allowed):
#allowed = set("ACGTacgt")
if set(read) <= allowed:
return True
else:
if verbose is True:
print("invalid read:")
print(read)
return False
def complement(s):
basecomplement = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A', 'a': 'T', 'c': 'G', 'g': 'C', 't': 'A'}
letters = list(s)
letters = [basecomplement[base] for base in letters]
return ''.join(letters)
def revcom(s):
return complement(s[::-1])
def create_random_readpairs(infile, readlength1, readlength2, gapsize, pos, verbose, allowed):
#try:
infile.seek(pos)
full_seq = infile.read(readlength1+gapsize+readlength2).replace('\n','').replace('\r','')
read1 = full_seq[0:readlength1] #todo: fit readlengths, they are 1 too long?
read2 = full_seq[-readlength2:]
#except:
# return False
if checkread(full_seq,verbose,allowed):
return read1, read2
def createrandomunassignedreads(infile, outfile1, outfile2, name, gapsize, verbose, chunk, amount, real_readfiles):
if chunk > amount:
chunk = amount
rest = chunk
revcomp = 0
filesize = os.path.getsize(infile)
infile = open(infile)
list1 = []
list2 = []
i = 0
sys.stdout.write("Simulating reads of "+name+" for evaluation:\n")
lengths = find_out_length(real_readfiles,amount,"fastq")
lengths1 = lengths[0]
lengths2 = lengths[1]
while rest > 0:
poslist = []
for j in range(rest+1):
poslist.append(random.randint(0, filesize-(lengths1[j]+lengths2[j]+gapsize)))
poslist = sorted(poslist)
for k in range(len(poslist)-1):
readlength1 = lengths1[i]
if SingleEnd:
readlength2 = 0
else:
readlength2 = lengths2[i]
reads = create_random_readpairs(infile,readlength1,readlength2,gapsize,poslist[k],verbose,allowed=set("ACGTacgt"))
###for fasta-reads
if reads:
i += 1
revcomp += 1
if revcomp % 2 == 0:
list1.append("".join([">",name , str(i), "\n" , reads[0], "\n"]))
list2.append("".join([">",name , str(i), "\n" , reads[1], "\n"]))
elif revcomp % 2 == 1:
list1.append("".join([">",name , str(i), "\n" , revcom(reads[0]), "\n"]))
list2.append("".join([">",name , str(i), "\n" , revcom(reads[1]), "\n"]))
if i%1000 == 0:
sys.stdout.write(str(float(i)/amount*100)+"%\r")
sys.stdout.flush()
else:
continue
###for fastq-reads
"""if reads:
i += 1
revcomp += 1
if revcomp % 2 == 0:
list1.append("".join(["@",name , str(i) , "\n" , reads[0] , "\n" , "+\n" , "#"*len(reads[0]) , "\n"]))
list2.append("".join(["@",name , str(i) , "\n" , reads[1] , "\n" , "+\n" , "#"*len(reads[1]) , "\n"]))
elif revcomp % 2 == 1:
list1.append("".join(["@",name , str(i) , "\n" , revcom(reads[0]) , "\n" , "+\n" , "#"*len(reads[0]) , "\n"]))
list2.append("".join(["@",name , str(i) , "\n" , revcom(reads[1]) , "\n" , "+\n" , "#"*len(reads[1]) , "\n"]))
if i%1000 == 0:
sys.stdout.write(str(float(i)/amount*100)+"%\r")
sys.stdout.flush()
else:
continue"""
for elem in range(len(list1)):
outfile1.write(list1[elem])
if not SingleEnd:
outfile2.write(list2[elem])
list1 = []
list2 = []
if rest < amount - i:
continue
else:
rest = amount - i
print("\n")
infile.close()
def createrandomassignedreads(infile, outfile1, outfile2, name, gapsize, verbose, chunk, amount, real_readfiles):
if chunk > amount:
chunk = amount
rest = chunk
revcomp = 0
filesize = os.path.getsize(infile)
infile = open(infile)
list1 = []
list2 = []
i = 0
sys.stdout.write("Simulating reads of "+name+" for training:\n")
lengths = find_out_length(real_readfiles,amount,"fastq")
while rest > 0:
poslist = []
for j in range(rest+1):
poslist.append(random.randint(0, filesize-(lengths[0][j]+lengths[1][j]+gapsize)))
poslist = sorted(poslist)
for k in range(len(poslist)-1):
readlength1 = lengths[0][i]
if SingleEnd:
readlength2 = 0
else:
readlength2 = lengths[1][i]
reads = create_random_readpairs(infile,readlength1,readlength2,gapsize,poslist[k],verbose,allowed=set("ACGTacgt"))
if reads:
i += 1
revcomp += 1
if revcomp % 2 == 0:
list1.append("".join([">",name , str(i) , "\n" , reads[0], "\n"]))
list2.append("".join([">",name , str(i) , "\n" , reads[1], "\n"]))
elif revcomp % 2 == 1:
list1.append("".join([">",name , str(i) , "\n" , revcom(reads[0]), "\n"]))
list2.append("".join([">",name , str(i) , "\n" , revcom(reads[1]), "\n"]))
if i%1000 == 0:
sys.stdout.write(str(float(i)/amount*100)+"%\r")
sys.stdout.flush()
else:
continue
for elem in range(len(list1)):
outfile1.write(list1[elem])
if not SingleEnd:
outfile2.write(list2[elem])
list1 = []
list2 = []
if rest < amount - i:
continue
else:
rest = amount - i
print("\n")
infile.close()
def main(infile1,infile2,name1,name2,temppath,real_readfiles,SE,amount,gapsize=1,verbose=False,chunk=100000):
global SingleEnd
SingleEnd=SE
if not SingleEnd:
outfile1 = os.path.join(temppath,"simulated_reads_"+name1+"_"+str(amount)+"_1.fasta")
outfile2 = os.path.join(temppath,"simulated_reads_"+name1+"_"+str(amount)+"_2.fasta")
outfile3 = os.path.join(temppath,"simulated_reads_"+name2+"_"+str(amount)+"_1.fasta")
outfile4 = os.path.join(temppath,"simulated_reads_"+name2+"_"+str(amount)+"_2.fasta")
outfile5 = os.path.join(temppath,"simulated_reads_"+name1+"_and_"+name2+"_"+str(amount)+"_1.fasta")
outfile6 = os.path.join(temppath,"simulated_reads_"+name1+"_and_"+name2+"_"+str(amount)+"_2.fasta")
outf1 = open(outfile1,"w")
outf2 = open(outfile2,"w")
outf3 = open(outfile3,"w")
outf4 = open(outfile4,"w")
else:
outfile1 = os.path.join(temppath,"simulated_reads_"+name1+"_"+str(amount)+".fasta")
outfile3 = os.path.join(temppath,"simulated_reads_"+name2+"_"+str(amount)+".fasta")
outfile5 = os.path.join(temppath,"simulated_reads_"+name1+"_and_"+name2+"_"+str(amount)+".fasta")
outf1 = open(outfile1,"w")
outf2 = None
outf3 = open(outfile3,"w")
outf4 = None
before = time.time()
createrandomassignedreads(infile1, outf1, outf2, name1, gapsize, verbose, chunk, amount, real_readfiles)
print(time.time()-before)
before = time.time()
createrandomassignedreads(infile2, outf3, outf4, name2, gapsize, verbose, chunk, amount, real_readfiles)
print(time.time()-before)
if not SingleEnd:
outf1.close()
outf2.close()
outf3.close()
outf4.close()
outf5, outf6 = open(outfile5,"w"), open(outfile6,"w")
else:
outf1.close()
outf3.close()
outf5 = open(outfile5,"w")
outf6 = None
#outf5, outf6 = open(outfile5,"w"), open(outfile6,"w")
before = time.time()
createrandomunassignedreads(infile1, outf5, outf6, name1, gapsize, verbose, chunk, amount, real_readfiles)
print(time.time()-before)
before = time.time()
createrandomunassignedreads(infile2, outf5, outf6, name2, gapsize, verbose, chunk, amount, real_readfiles)
print(time.time()-before)
if not SingleEnd:
outf5.close()
outf6.close()
else:
outf5.close()
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('-i', '--infile', help='Input file of species 1 and species 2, given in fasta-format', required=True, action='append')
parser.add_argument('-r', '--real_readfiles', help='One File containing a subset of your reads in fastq-format', required=True, action='append')
parser.add_argument('-n', '--name', help='Name of species 1 and species 2', required=True, action='append')
parser.add_argument('-o', '--outpath', help='Path to write resulting files', required=True)
parser.add_argument('-g', '--gapsize', help='Approximate lenght of gap between reads', required=False, default=0)
parser.add_argument('-v', '--verbose', help='print invalid reads and additional information',required=False,default=False,action='store_true')
parser.add_argument('-a', '--amount', help='number of reads to be simulated for all kinds', required=False,default=500000)
parser.add_argument('-c', '--chunk', help='number of reads to be generated before writing. Choose according to your RAM.', required=False,default=100000)
parser.add_argument('-s', '--SE', help='Single End mode', action='store_true', default=False)
args = parser.parse_args()
verbose = args.verbose
outpath = str(args.outpath)
amount = int(args.amount)
chunk = int(args.chunk)
SE = args.SE
if SE:
gapsize = 0
else:
gapsize = int(args.gapsize)
infile1 = args.infile[0]
infile2 = args.infile[1]
name1 = str(args.name[0])
name2 = str(args.name[1])
real_readfiles = args.real_readfiles
main(infile1,infile2,name1,name2,outpath,real_readfiles,SE,amount,gapsize,verbose,chunk)
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