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teflon.v0.4.py
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teflon.v0.4.py
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# -*- coding: utf-8 -*-
"""
Created on Tue Feb 16 15:29:00 2016
@author: jeffreyadrion
"""
import argparse, sys, os
import multiprocessing as mp
import subprocess as sp
import shlex
import glob
import shutil
teflonBase = os.path.dirname(os.path.abspath(sys.argv[0]))
sys.path.insert(1, teflonBase)
from teflon_scripts import write_bed as wb
from teflon_scripts import cluster_positions as cp
from teflon_scripts import position_estimate as pe
from teflon_scripts import sort_positions as sortp
def progress_bar(percent, barLen = 50):
sys.stdout.write("\r")
progress = ""
for i in range(barLen):
if i < int(barLen * percent):
progress += "="
else:
progress += " "
sys.stdout.write("[ %s ] %.2f%%" % (progress, percent * 100))
sys.stdout.flush()
def mkdir_if_not_exist(*dirs):
for dir in dirs:
if not os.path.exists(dir):
os.makedirs(dir)
print "creating directory: %s" %(dir)
def check_dependency(exeSAM):
try:
cmd = "%s" %(exeSAM)
sp.Popen(shlex.split(cmd), stdout=sp.PIPE, stderr=sp.PIPE)
except OSError:
print "Cannot find %s" %(exeSAM)
sys.exit(1)
def assign_task(siteID, task_q, nProcs):
c,i,nth_job=0,0,1
while (i+1)*nProcs <= len(siteID):
i+=1
nP1=nProcs-(len(siteID)%nProcs)
for j in range(nP1):
task_q.put((siteID[c:c+i], nth_job))
nth_job += 1
c=c+i
for j in range(nProcs-nP1):
task_q.put((siteID[c:c+i+1], nth_job))
nth_job += 1
c=c+i+1
def create_proc2(nProcs, task_q, params):
for _ in range(nProcs):
p = mp.Process(target=worker2, args=(task_q, params))
p.daemon = True
p.start()
def create_proc3(nProcs, task_q, params):
for _ in range(nProcs):
p = mp.Process(target=worker3, args=(task_q, params))
p.daemon = True
p.start()
def worker2(task_q, params):
while True:
try:
groups, nth_job = task_q.get()
#unpack parameters
annotation, bam, chromosomes, exeSAM, hierarchy, insz, label, lengths, level, cLevel, qual, readLen, sd, cov, bedDir, samDir, posDir, suppDir = params
ct=1
for group in groups:
# 2. samtools view > complete.sam
try:
samFile_complete = os.path.join(samDir, "%s_complete.sam" %(group))
cmd = "%s view %s -L %s/%s_complete.bed" %(exeSAM, bam, bedDir, group)
#print "cmd:", cmd
p = sp.Popen(shlex.split(cmd), stdout=open(samFile_complete, 'w'), stderr=sp.PIPE)
perr = p.communicate()[1] # communicate returns a tuple (stdout, stderr)
#print perr
if p.returncode != 0:
print "error running samtools"
sys.exit(1)
except OSError:
print "Cannot run samtools"
sys.exit(1)
# 3. cluster positions
suppOutFile = os.path.join(suppDir, "%s_supplemental_alignments.txt" %(group))
cp.cluster_positions_portal(samFile_complete, group, chromosomes, lengths, readLen, insz, sd, bedDir, qual, suppOutFile)
if nth_job==1:
progress_bar(ct/float(len(groups)))
ct+=1
finally:
task_q.task_done()
def worker3(task_q, params):
while True:
try:
groups, nth_job = task_q.get()
#unpack parameters
annotation, bam, chromosomes, exeSAM, hierarchy, insz, label, lengths, level, cLevel, qual, readLen, sd, cov, bedDir, samDir, posDir, suppDir = params
ct=1
for group in groups:
teIDs=[]
bed=os.path.join(bedDir,group+"_complete.bed")
with open(bed, "r") as fIN:
for line in fIN:
teIDs.append(line.split()[0])
levelIndex=label.index(level)
clustIndex=label.index(cLevel)
clustGroup=""
for ID in hierarchy:
if hierarchy[ID][levelIndex] == group:
clustGroup=hierarchy[ID][clustIndex]
break
suppOutFile = os.path.join(suppDir, "%s_supplemental_alignments.txt" %(group))
#4. samtools view > clustered.sam
try:
samFile_clust = os.path.join(samDir, "%s_clustered.sam" %(group))
cmd = "%s view %s -L %s/%s_clustered.bed" %(exeSAM, bam, bedDir, group)
#print "cmd:", cmd
p = sp.Popen(shlex.split(cmd), stdout=open(samFile_clust, 'w'), stderr=sp.PIPE)
# communicate returns a tuple (stdout, stderr)
perr = p.communicate()[1]
#print perr
if p.returncode != 0:
print "error running samtools"
sys.exit(1)
except OSError:
print "Cannot run samtools"
sys.exit(1)
#5. position estimate
pe.position_estimate_portal(samFile_clust, suppOutFile, group, annotation, teIDs, readLen, insz, sd, cov, posDir, clustGroup, hierarchy)
if nth_job==1:
progress_bar(ct/float(len(groups)))
ct+=1
finally:
task_q.task_done()
def main():
parser = argparse.ArgumentParser()
parser.add_argument('-wd',dest='wd',help='full path to working directory',default=-1)
parser.add_argument('-d',dest='DIR',help='full path to prep_TF directory')
parser.add_argument('-s',dest='samples',help='samples file')
parser.add_argument('-i',dest='ID',help='unique id of this sample')
parser.add_argument('-eb',dest='exeBWA',help='full path to bwa executable', default="bwa")
parser.add_argument('-es',dest='exeSAM',help='full path to samtools executable', default="samtools")
parser.add_argument('-l1',dest='level',help='level of hierarchy to guide initial search')
parser.add_argument('-l2',dest='cLevel',help='level of hierarchy to cluster')
parser.add_argument('-q',dest='qual',help='map quality threshold',type=int)
parser.add_argument('-exclude',dest='exclude',help='newline separated list of te families to exclude from analysis', default=-1)
parser.add_argument('-sd',dest='stdev',help='insert size standard deviation override',type=int, default=-1)
parser.add_argument('-cov',dest='cov',help='manual coverage override',type=int, default=-1)
parser.add_argument("-t", dest="nProc", type=int, default=1, help="Specify number of processes")
args = parser.parse_args()
# identify current working directory
if args.wd == -1:
cwd=os.getcwd()
else:
cwd=os.path.abspath(args.wd)
# import options
prep_TF=os.path.abspath(args.DIR)
prefix=os.path.abspath(args.DIR).split("/")[-1].replace(".prep_TF","")
exeSAM=args.exeSAM
exeBWA=args.exeBWA
level=args.level
cLevel=args.cLevel
qual=args.qual
nProc=args.nProc
# check dependencies for function
check_dependency(exeSAM)
check_dependency(exeBWA)
# import hierarchy
hierFILE=os.path.join(prep_TF,prefix+".hier")
hierarchy,label={},[]
ct=0
with open(hierFILE, 'r') as fIN:
for line in fIN:
if ct==0:
label=line.split()[1:]
else:
hierarchy[line.split()[0]] = line.split()[1:]
ct+=1
bam,pre="",""
with open(os.path.abspath(args.samples), "r") as fIN:
for line in fIN:
if line.split()[1] == args.ID:
pre = line.split()[1]
bam = line.split()[0]
if pre=="" or bam=="":
print "Warning: prefix in samples file different from path in options"
sys.exit()
# identify the group-name of all TEs for the specified level of the hierarchy
groups=[]
groupIndex=label.index(level)
for ID in hierarchy:
groups.append(hierarchy[ID][groupIndex])
groups=sorted(set(groups))
# import the TE annotation
annotation=[]
with open(os.path.join(prep_TF,prefix+".te.pseudo.bed"), 'r') as fIN:
for line in fIN:
arr=line.split()
annotation.append([arr[0],int(arr[1]),int(arr[2]),arr[3]])
# import the chromosome lengths
chromosomes,lengths=[],[]
genomeSizeFILE=os.path.join(prep_TF,prefix+".genomeSize.txt")
with open(genomeSizeFILE, 'r') as fIN:
for line in fIN:
arr=line.split()
chromosomes.append(arr[0])
lengths.append(int(arr[2]))
# run samtools stats
statsOutFile = bam.replace(".bam", ".stats.txt")
print "Calculating alignment statistics"
cmd = "%s stats -t %s %s" %(exeSAM, genomeSizeFILE, bam)
print "cmd:",cmd
p = sp.Popen(shlex.split(cmd), stdout=open(statsOutFile, 'w'), stderr=sp.PIPE)
perr = p.communicate()[1]
if p.returncode != 0:
print "samtools stats issued error: %s" %(perr)
sys.exit(1)
# calculate coverage
covFILE = bam.replace(".bam", ".cov.txt")
cmd="""%s depth -Q %s %s | awk '{sum+=$3; sumsq+=$3*$3} END {print "Average = ",sum/NR; print "Stdev = ",sqrt(sumsq/NR - (sum/NR)**2)}' > %s""" %(exeSAM, str(qual), bam, covFILE)
print "cmd:",cmd
os.system(cmd)
# read samtools stats file
with open(statsOutFile, 'r') as fIN:
for line in fIN:
if 'average length' in line:
readLen=int(float(line.split()[-1]))
if 'insert size average' in line:
insz=int(float(line.split()[-1]))
if 'insert size standard deviation' in line:
sd=int(float(line.split()[-1]))
if args.stdev == -1:
print "Insert size standard deviation estimated as %s. Use the override option if you suspect this is incorrect!" %(sd)
if sd > 100:
print "!!! Warning: insert size standard deviation reported as",sd,"!!!"
print "Please ensure this is correct and use the override option!"
sys.exit()
else:
sd=args.stdev
# read coverage file
cov=args.cov
with open(covFILE, "r") as fIN:
for line in fIN:
if line.startswith("Av"):
cov=int(float(line.split()[-1]))
if cov == -1:
print "Warning: coverage could not be estimated, enter coverage manually"
sys.exit()
# read list of TE groups to exclude from analysis
if args.exclude == -1:
excludeList=[]
else:
excludeList=[]
with open(args.exclude, "r") as fIN:
for line in fIN:
excludeList.append(line.split()[0])
# define and create subdirectories
bedDir = os.path.join(cwd,pre+".bed_files")
samDir = os.path.join(cwd,pre+".sam_files")
posDir = os.path.join(cwd,pre+".te_positions")
suppDir = os.path.join(cwd,pre+".supplemental_alignments")
outDir = os.path.join(cwd,"countPos")
mkdir_if_not_exist(bedDir, posDir, samDir, suppDir, outDir)
groups = [group for group in groups if group not in excludeList]
#groups= ["doc3"] #debug single family
print "Groups to search:", groups
print "\nwriting TE bed files..."
for group in groups:
#print "group:",group
wb.write_bed_portal(hierarchy, label, group, level, bedDir)
print "writing TE bed files completed!"
# reduce search-space 1
print "reducing search space..."
try:
bedFILE = os.path.join(bedDir,"mega_complete.bed")
bamFILE = os.path.join(samDir,"mega_complete.bam")
cmd = "%s view -@ %s -L %s %s -b" %(exeSAM, str(nProc), bedFILE, bam)
print "cmd:", cmd
p = sp.Popen(shlex.split(cmd), stdout=open(bamFILE, 'w'), stderr=sp.PIPE)
perr = p.communicate()[1] # communicate returns a tuple (stdout, stderr)
#print perr
if p.returncode != 0:
print "Error running samtools: p.returncode =",p.returncode
sys.exit(1)
except OSError:
print "Cannot run samtools"
print "search space succesfully reduced..."
print "new reduced bam file:",bamFILE
# run multiprocess 2
print "clustering TE positions..."
task_q = mp.JoinableQueue()
params=[annotation, bamFILE, chromosomes, exeSAM, hierarchy, insz, label, lengths, level, cLevel, qual, readLen, sd, cov, bedDir, samDir, posDir, suppDir]
create_proc2(nProc, task_q, params)
assign_task(groups, task_q, nProc)
try:
task_q.join()
except KeyboardInterrupt:
print "KeyboardInterrupt"
sys.exit(0)
else:
print "\nclustering TE positions completed!"
# combine bed files from all groups
with open(os.path.join(bedDir, "mega_clustered.bed"),"w") as fOUT:
for group in groups:
with open(os.path.join(bedDir, "%s_clustered.bed" %(group)), "r") as fIN:
for line in fIN:
fOUT.write(line)
# reduce search-space 2
print "final reduction of search space..."
try:
bedFILE = os.path.join(bedDir,"mega_clustered.bed")
bamFILE = os.path.join(samDir,"mega_clustered.bam")
cmd = "%s view -@ %s -q %s -L %s %s -b" %(exeSAM, str(nProc), str(qual), bedFILE, bam)
print "cmd:", cmd
p = sp.Popen(shlex.split(cmd), stdout=open(bamFILE, 'w'), stderr=sp.PIPE)
perr = p.communicate()[1] # communicate returns a tuple (stdout, stderr)
#print perr
if p.returncode != 0:
print "Error running samtools: p.returncode =",p.returncode
sys.exit(1)
except OSError:
print "Cannot run samtools"
print "search space succesfully reduced..."
print "new reduced bam file:",bamFILE
# run multiprocess 3
print "estimating TE breakpoints..."
bamFILE = os.path.join(samDir,"mega_clustered.bam")
task_q = mp.JoinableQueue()
params=[annotation, bamFILE, chromosomes, exeSAM, hierarchy, insz, label, lengths, level, cLevel, qual, readLen, sd, cov, bedDir, samDir, posDir, suppDir]
create_proc3(nProc, task_q, params)
assign_task(groups, task_q, nProc)
try:
task_q.join()
except KeyboardInterrupt:
print "KeyboardInterrupt"
sys.exit(0)
else:
print "\nestimating TE breakpoints completed!"
# concatonate position estimates
catFile = os.path.join(outDir,pre + ".all_positions.txt")
try:
files = ""
for file in glob.glob(os.path.join(posDir, "*.txt")):
files += file + " "
cmd = "cat %s" %(files)
#print "cmd:", cmd #p = sp.Popen(shlex.split(cmd), stdout=open(catFile, 'w'), stderr=sp.PIPE)
p = sp.Popen(shlex.split(cmd), stdout=open(catFile, 'w'), stderr=sp.PIPE)
perr = p.communicate()[1] # communicate returns a tuple (stdout, stderr)
#print perr
if p.returncode != 0:
print "error concatenating positions"
sys.exit(1)
except OSError:
print "Cannot concatenate positions"
sys.exit(1)
# sort position estimates
print "Sorting positions..."
sortp.sort_portal(catFile)
# remove temporary directories
shutil.rmtree(bedDir)
shutil.rmtree(samDir)
shutil.rmtree(posDir)
shutil.rmtree(suppDir)
print "TEFLON DISCOVERY FINISHED!"
if __name__ == "__main__":
main()