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1ParallelParser.py
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1ParallelParser.py
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#######################################################################
##
## ParallelParser.py
##
## Version 1.00 -- 11 July 2013
##
## Created by Michael Sorenson
## Copyright (c) 2011-2013 Boston University. All rights reserved.
##
## Dependencies: specs file (see example.specs)
## ddRADparser.py
## CondenseSequences.py
## FilterSequences.py
##
## This program is written for execution in the python (version 3)
## language, and uses the multiprocessing module and ssh to run
## parallel jobs in a Diskless Remote Boot Linux (DRBL) environment.
## It is free and distributed WITHOUT warranty; without
## even the implied warranty of MERCHANTABILITY or FITNESS FOR A
## PARTICULAR PURPOSE.
##
#######################################################################
import sys
import os
import subprocess
import multiprocessing
from multiprocessing import Process, Lock
def start_run(cmd):
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
RADspecs_file = open(sys.argv[1], 'r')
#get info from RADspecs file
line = RADspecs_file.readline()
data = line.split()
if data[1]=='2':
Paired = True
else:
Paired = False
line = RADspecs_file.readline()
data = line.split('\t')
path = data[1]
line = RADspecs_file.readline()
line = RADspecs_file.readline()
data = line.split()
basefilename1 = data[1]
qseq_file1 = open(path+data[1]+'.qseq','r')
line = RADspecs_file.readline()
if Paired == True:
data = line.split()
basefilename2 = data[1]
qseq_file2 = open(path+data[1]+'.qseq','r')
line = RADspecs_file.readline()
data = line.split()
barcode_file = open(path+data[1],'r')
RADspecs_file.readline()
RADspecs_file.readline()
RADspecs_file.readline()
line = RADspecs_file.readline()
data = line.split()
r_site1_complete_length = len(data[1])
for i in range(5):
line = RADspecs_file.readline()
data = line.split()
nruns = int(data[1])
print("N_processes: ",nruns)
line = RADspecs_file.readline()
hosts = []
for i in range(nruns):
line = RADspecs_file.readline()
data = line.split()
hosts.append(data[0])
hosts3 = hosts*3
#length of input files
cmd = ('wc -l '+path+basefilename1+'.qseq')
p = subprocess.getoutput(cmd)
file_data = p.split()
file_length = int(file_data[0])
target_length = round((file_length/(nruns*3))+1)
if Paired == True:
#create input files - including multiple specs files
line_count = 0
file_count = 101
target = target_length
outfile1 = open(path+basefilename1+str(file_count)+'.qseq','w')
outfile2 = open(path+basefilename2+str(file_count)+'.qseq','w')
for line1 in qseq_file1:
line2 = qseq_file2.readline()
line_count += 1
outfile1.write(line1)
outfile2.write(line2)
if line_count == target:
outfile1.close()
outfile2.close()
cmd = ('cp '+sys.argv[1]+' temp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename1+'/'+basefilename1+str(file_count)+'/ <temp >temp2')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename2+'/'+basefilename2+str(file_count)+'/ <temp2 >'+path+sys.argv[1]+str(file_count))
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
file_count+=1
target += target_length
outfile1 = open(path+basefilename1+str(file_count)+'.qseq','w')
outfile2 = open(path+basefilename2+str(file_count)+'.qseq','w')
outfile1.close()
outfile2.close()
cmd = ('cp '+sys.argv[1]+' temp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename1+'/'+basefilename1+str(file_count)+'/ <temp >temp2')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename2+'/'+basefilename2+str(file_count)+'/ <temp2 >'+path+sys.argv[1]+str(file_count))
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm temp temp2')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
#launch runs
threads=[]
if __name__ == '__main__':
lock = Lock()
for i in range(nruns*3):
if len(threads) < nruns:
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'ddRADparser.py '+path+sys.argv[1]+str(101+i)+' '+str(101+i))
print(cmd)
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
else:
while len(threads) == nruns:
tnum = -1
for thread in threads:
tnum += 1
if not thread.is_alive():
threads.remove(thread)
hosts.append(hosts.pop(tnum))
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'ddRADparser.py '+path+sys.argv[1]+str(101+i)+' '+str(101+i))
print(cmd)
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
while len(threads) > 0:
for thread in threads:
if not thread.is_alive():
threads.remove(thread)
#concatenate files
samples=[]
for line in barcode_file:
data = line.split()
samples.append(data[2])
num_samples = len(samples)
for i in range(num_samples):
cmd = ('cat '+path+samples[i]+'R11*qseq > '+path+samples[i]+'R1.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+samples[i]+'R11*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+samples[i]+'R21*qseq > '+path+samples[i]+'R2.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+samples[i]+'R21*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'TinyR1seqs1* > '+path+'TinyR1seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'TinyR1seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'TinyR2seqs1* > '+path+'TinyR2seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'TinyR2seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'UnassignedR1seqs1* > '+path+'UnassignedR1seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'UnassignedR1seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'UnassignedR2seqs1* > '+path+'UnassignedR2seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'UnassignedR2seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'ConcatamerR1seqs1* > '+path+'ConcatamerR1seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'ConcatamerR1seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'ConcatamerR2seqs1* > '+path+'ConcatamerR2seqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'ConcatamerR2seqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+basefilename1+'1*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+basefilename2+'1*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+sys.argv[1]+'1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
summ_data = []
inputfile = open(path+basefilename1+str(101)+'summary.out')
for line in inputfile:
data = line.strip('\n').split('\t')
summ_data.append(data)
for i in range(nruns-1):
inputfile = open(path+basefilename1+str(102+i)+'summary.out')
inputfile.readline()
line_count=0
for line in inputfile:
line_count+=1
data = line.strip('\n').split('\t')
for j in range(1,len(data)):
summ_data[line_count][j] = int(summ_data[line_count][j])+int(data[j])
outputfile = open(path+basefilename1+'summary.out','w')
for i in range(len(summ_data)):
outputfile.write(str(summ_data[i][0]))
for j in range(1,len(summ_data[i])):
outputfile.write('\t'+str(summ_data[i][j]))
outputfile.write('\n')
outputfile.close()
cmd = ('rm '+path+basefilename1+'1*summary*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
bstart = []
bstart_counts= []
for i in range(nruns):
inputfile = open(path+'Unassigned_start_seqs'+str(101+i)+'.out')
inputfile.readline()
for line in inputfile:
data = line.strip('\n').split('\t')
if data[0] in bstart:
bstart_counts[bstart.index(data[0])] += int(data[1])
else:
bstart.append(data[0])
bstart_counts.append(int(data[1]))
outputfile = open(path+'Unassigned_start_seqs.out','w')
outputfile.write('Sequence\tCount\n')
for i in range(len(bstart)):
outputfile.write(bstart[i]+'\t'+str(bstart_counts[i])+'\n')
outputfile.close()
cmd = ('rm '+path+'Unassigned_start_seqs1*.out')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
##
## starts here for single read processing
##
else:
#create input files - including multiple specs files
line_count = 0
file_count = 101
print("Generating Files")
print(file_count)
target = target_length
outfile1 = open(path+basefilename1+str(file_count)+'.qseq','w')
for line1 in qseq_file1:
line_count += 1
outfile1.write(line1)
if line_count == target:
outfile1.close()
cmd = ('cp '+sys.argv[1]+' temp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename1+'/'+basefilename1+str(file_count)+'/ <temp >'+path+sys.argv[1]+str(file_count))
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
file_count+=1
target += target_length
outfile1 = open(path+basefilename1+str(file_count)+'.qseq','w')
print(file_count)
outfile1.close()
cmd = ('cp '+sys.argv[1]+' temp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('sed s/'+basefilename1+'/'+basefilename1+str(file_count)+'/ <temp >'+path+sys.argv[1]+str(file_count))
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm temp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
#launch runs
threads=[]
if __name__ == '__main__':
lock = Lock()
for i in range(nruns*3):
if len(threads) < nruns:
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'ddRADparser.py '+path+sys.argv[1]+str(101+i)+' '+str(101+i))
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
else:
while len(threads) == nruns:
tnum = -1
for thread in threads:
tnum += 1
if not thread.is_alive():
threads.remove(thread)
hosts.append(hosts.pop(tnum))
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'ddRADparser.py '+path+sys.argv[1]+str(101+i)+' '+str(101+i))
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
while len(threads) > 0:
for thread in threads:
if not thread.is_alive():
threads.remove(thread)
#concatenate files
samples=[]
for line in barcode_file:
data = line.split()
samples.append(data[2])
num_samples = len(samples)
for i in range(num_samples):
cmd = ('cat '+path+samples[i]+'1*qseq > '+path+samples[i]+'.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+samples[i]+'1*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'TinySeqs1* > '+path+'TinySeqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'TinySeqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'UnassignedSeqs1* > '+path+'UnassignedSeqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'UnassignedSeqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('cat '+path+'ConcatamerSeqs1* > '+path+'ConcatamerSeqs.qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+'ConcatamerSeqs1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+basefilename1+'1*qseq')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
cmd = ('rm '+path+sys.argv[1]+'1*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
summ_data = []
inputfile = open(path+basefilename1+str(101)+'summary.out')
for line in inputfile:
data = line.strip('\n').split('\t')
summ_data.append(data)
for i in range(nruns*3-1):
inputfile = open(path+basefilename1+str(102+i)+'summary.out')
inputfile.readline()
line_count=0
for line in inputfile:
line_count+=1
data = line.strip('\n').split('\t')
for j in range(1,len(data)):
summ_data[line_count][j] = int(summ_data[line_count][j])+int(data[j])
outputfile = open(path+basefilename1+'summary.out','w')
for i in range(len(summ_data)):
outputfile.write(str(summ_data[i][0]))
for j in range(1,len(summ_data[i])):
outputfile.write('\t'+str(summ_data[i][j]))
outputfile.write('\n')
outputfile.close()
cmd = ('rm '+path+basefilename1+'1*summary*')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
bstart = []
bstart_counts= []
for i in range(nruns*3):
inputfile = open(path+'Unassigned_start_seqs'+str(101+i)+'.out')
inputfile.readline()
for line in inputfile:
data = line.strip('\n').split('\t')
if data[0] in bstart:
bstart_counts[bstart.index(data[0])] += int(data[1])
else:
bstart.append(data[0])
bstart_counts.append(int(data[1]))
outputfile = open(path+'Unassigned_start_seqs.out','w')
outputfile.write('Sequence\tCount\n')
for i in range(len(bstart)):
outputfile.write(bstart[i]+'\t'+str(bstart_counts[i])+'\n')
outputfile.close()
cmd = ('rm '+path+'Unassigned_start_seqs1*.out')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
#run CondenseSequences.py
threads=[]
for i in range(num_samples):
if len(threads) < nruns:
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'CondenseSequences.py '+path+samples[i]+'.qseq '+str(r_site1_complete_length))
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
else:
while len(threads) == nruns:
tnum = -1
for thread in threads:
tnum += 1
if not thread.is_alive():
threads.remove(thread)
hosts.append(hosts.pop(tnum))
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'CondenseSequences.py '+path+samples[i]+'.qseq '+str(r_site1_complete_length))
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
while len(threads) > 0:
for thread in threads:
if not thread.is_alive():
threads.remove(thread)
inputfile = open(path+basefilename1+'summary.out','r')
line = inputfile.readline()
outputfile = open(path+basefilename1+'sumtemp.out','w')
outputfile.write(line)
for i in range(num_samples):
inputfile2 = open(path+samples[i]+'.sumtemp','r')
line2=inputfile2.readline()
data2 = line2.split()
line = inputfile.readline()
data = line.split()
data.insert(6,data2[2])
outputfile.write('\t'.join(data)+'\n')
cmd = ('rm '+path+samples[i]+'.sumtemp')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
for i in range(4):
line = inputfile.readline()
outputfile.write(line)
outputfile.close()
cmd = ('mv '+path+basefilename1+'sumtemp.out '+path+basefilename1+'summary.out')
p = subprocess.Popen(cmd, shell=True)
sts = os.waitpid(p.pid, 0)[1]
#run FilterSequences.py
threads=[]
for i in range(num_samples):
if len(threads) < nruns:
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'FilterSequences.py '+path+samples[i]+'C.qseq')
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
else:
while len(threads) == nruns:
tnum = -1
for thread in threads:
tnum += 1
if not thread.is_alive():
threads.remove(thread)
hosts.append(hosts.pop(tnum))
cmd = ('ssh '+hosts[len(threads)]+' python3 '+path+'FilterSequences.py '+path+samples[i]+'C.qseq')
p = multiprocessing.Process(target=start_run,args=[cmd])
p.start()
threads.append(p)
while len(threads) > 0:
for thread in threads:
if not thread.is_alive():
threads.remove(thread)