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ublastx64ram.py
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ublastx64ram.py
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from Bio import SeqIO
import sys
import os
from StringIO import StringIO # Python 2
import subprocess
from random import randrange
if os.path.isfile('/db2/genpept.udb')== False:
print "loading db to ram"
subprocess.Popen("sudo mkdir -p /db2 && sudo mount -t tmpfs tmpfs /db2 && sudo chmod 777 /db2 && cp -n ~/data/db/genpept/genpept.udb /db2/genpept.udb", shell=True).wait()
else:
print "db already exists"
def chunkstring(string, length):
return (string[0+i:length+i] for i in range(0, len(string), length))
inputfile = sys.argv[1]
outputfile=sys.argv[2]
chunksize = int(str(sys.argv[3])) #number of reads in each division of the input file
threads = int(sys.argv[4])
fmt = sys.argv[5] #input format
fetchsize = sys.argv[6]
maxhits = sys.argv[7]
meta=sys.argv[8]
r2=str(randrange(100000))
subprocess.Popen("rm -rf ~/scripts/tmp2", shell=True).wait()
subprocess.Popen("mkdir ~/scripts/tmp2", shell=True).wait()
out1=open('/OSM/HOME-MEL/all29c/scripts/tmp2/finaloutput%s.ublast' %(r2),'w')
f2=open('/OSM/HOME-MEL/all29c/scripts/tmp2/inp%s.fa' %(r2),'w')
#split large reads/contigs if >50kb
print "splitting large seq records if >50kb..."
for i in SeqIO.parse(inputfile,fmt):
if len(i.seq)>50000:
seqlist=list(chunkstring(i.seq,50000))
c=-1
for t in seqlist:
c=c+1
print i.id, c+1
f2.write(">"+i.id+"-part-"+str(c+1)+"\n"+str(t)+"\n")
else:
f2.write(">"+i.id+"\n"+str(i.seq)+"\n")
f2.close()
inputfile2=open('/OSM/HOME-MEL/all29c/scripts/tmp2/inp%s.fa' %(r2),'r')
count = SeqIO.index('/OSM/HOME-MEL/all29c/scripts/tmp2/inp%s.fa' %(r2), fmt)
c= len(count)
#print c
a= int(c)
print "num reads=",a
if chunksize>a:
chunksize=a
numchunks = (a/chunksize)
#print"Number of chunks=",numchunks
#sys.stdout.write(str(numchunks))
t=0
f=1
print"Writing split files..."
outfile = "/OSM/HOME-MEL/all29c/scripts/tmp2/%subin" %(r2)+str(f)+".fna"
g=open(outfile,'w')
for i in SeqIO.parse(inputfile2,fmt):
t=t+1
if t>chunksize:
f=f+1
outfile = "/OSM/HOME-MEL/all29c/scripts/tmp2/%subin" %(r2)+str(f)+".fna"
g=open(outfile,'w')
t=1
#print"file",f,"record",t
#print i.seq
#raw_input()
SeqIO.write(i,g,"fasta")
print "Number of chunks=",numchunks
print "Files written"
print "Multithreading ublast"
#numt = number of times to run multithread
p1=[];p2=[];p3=[];p4=[];p5=[]
q=0
numreps = int(numchunks/threads)
if numreps<1:
numreps=1
threads=numchunks
for setp in range(1,threads+2):
p1.append("")
print len(p1),"lenp1"
for rep in range(1,numreps+1):
for x in range(1,threads+1):
q=q+1 #file number
p1[x] = subprocess.Popen("usearch -ublast ~/scripts/tmp2/%subin%d.fna -db /db2/genpept.udb -evalue 1e-10 -accel 0.5 -maxhits %s -maxaccepts 100 -maxrejects 1024 -userout ~/scripts/tmp2/%subin%dout.txt -userfields query+target+id+ql+qlo+qhi+tlo+thi+tl+alnlen+evalue+bits" %(r2,q,maxhits,r2,q), shell=True)
#wait for n threads to finish
for x1 in range(1,threads+1):
print "waiting for usearch to finish........."
p1[x1].wait()
for x2 in range(1,threads+1):
print "concatenating.....", x2
if meta =="m":
subprocess.Popen("cat ~/scripts/tmp2/%subin%dout.txt >> ~/scripts/tmp2/finaloutput%s.ublast" %(r2,x2,r2), shell=True).wait()
else:
subprocess.Popen("cat ~/scripts/tmp2/%subin%dout.txt >> %s" %(r2,x2,outputfile), shell=True).wait()
#subprocess.Popen("rm -rf ~/scripts/tmp2/ubin* ~/scripts/tmp2/1ubin* ~/scripts/tmp2/2ubin* ~/scripts/tmp2/3ubin* ~/scripts/tmp2/4ubin* ~/scripts/tmp2/5ubin* ", shell=True).wait()
if meta =="m":
print"adding taxonomy.."
subprocess.Popen("python ~/scripts/taxonfetch.py ~/scripts/tmp2/finaloutput%s.ublast %s p %s" %(r2,outputfile,fetchsize), shell=True).wait()
#############otufreq.py
f2 = open(outputfile,'r')
g2=open(outputfile+".species",'w')
g3=open(outputfile+".genera",'w')
# read output file species into list
species=[]
genus=[]
k=[]
print "Getting species.."
for line in f2:
k=line.rstrip("\n").split("\t")[13].split(" ")
print k
if len(k)>1:
species.append(" ".join(str(x5) for x5 in k[0:2])) #nb makes two element list into a single string
if len(k)==1:
species.append(k[0])
genus.append(line.split("\t")[13].split(" ")[0])
species_set=set(species)
genus_set=set(genus)
print "Counting species.."
for i in species_set:
g2.write(i+"\t"+str(species.count(i))+"\n")
for i in genus_set:
g3.write(i+"\t"+str(genus.count(i))+"\n")
subprocess.Popen("rm /OSM/HOME-MEL/all29c/scripts/tmp2/finaloutput%s.ublast" %(r2), shell=True).wait()
subprocess.Popen("rm /OSM/HOME-MEL/all29c/scripts/tmp2/inp%s.fa" %(r2), shell=True).wait()
subprocess.Popen("rm -r /OSM/HOME-MEL/all29c/scripts/tmp2/%subin*" %(r2), shell=True).wait()
f2.close()
g2.close()
g3.close()