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isvda.py
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isvda.py
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#!/usr/bin/python
"""
Author: Chen Sun, chensun@cse.psu.edu
"""
import sys
versionError = "You are using an old version of python, please upgrade to python 2.7+\n"
if sys.hexversion < 0x02070000:
print (versionError)
#elif sys.hexversion > 0x03000000:
# print ("python 3")
import subprocess, argparse, os
from datetime import datetime
from multiprocessing import Pool
import time
citation = "Please cite our paper."
DEBUG = False
RUN = True
def shell_run(command):
if not RUN:
time.sleep(5.7)
print (command)
else:
print (command)
print (".")
subprocess.call(command, shell=True)
def serial_exe(command_list):
#print 'running serial_exe: ', command_list
for command in command_list:
shell_run(command)
def check_command(command):
"""
check if corresponding command available
"""
if os.path.isfile(command):
return True
for cmdpath in os.environ['PATH'].split(':'):
if os.path.isdir(cmdpath) and command in os.listdir(cmdpath):
return True
return False
parser = argparse.ArgumentParser(epilog = citation)
parser.add_argument('-r', '--reference', required=not DEBUG, default = '/gpfs/home/cxs1031/standard/repairing/bacteria/ref.fa', help = 'reference genome file path')
parser.add_argument('-p', '--pair_end', required=not DEBUG, nargs = 2, default = '/gpfs/home/cxs1031/standard/repairing/bacteria/donor_10x_1.fq /gpfs/home/cxs1031/standard/repairing/bacteria/donor_10x_2.fq'.split(), help = 'two pair end read files')
parser.add_argument('-i', '--iteration', required=not DEBUG, default = 4, type = int, help = 'number of iteration to run, if not detect new high confident snp, the pipeline will terminate automatically, even there are still iterations left')
parser.add_argument('-w', '--workspace', required=not DEBUG, default='/gpfs/home/cxs1031/standard/repairing/bacteria', help = 'directory where result will be put in, should be empty')
parser.add_argument('-o', '--output', help = 'snp result file in vcf file format')
parser.add_argument('-t', '--thread', default=1, type=int, help = 'multi-thread number to run each step that can be paralleled')
#parser.add_argument('-k', action='store_true')
parser.add_argument('--bwa', default='bwa', help = 'bwa program path')
parser.add_argument('-e', help='use bowtie instead of bwa, default is deactivte', action='store_true')
parser.add_argument('--bowtie', default='bowtie2', help = 'bowtie2 program path')
parser.add_argument('--bindex', default='bowtie2-build', help = 'bowtie2-build program path')
parser.add_argument('--samtools', default='samtools', help = 'samtools program path')
parser.add_argument('--python', default='python', help = 'python program path')
parser.add_argument('--parallel_freebayes', required=not DEBUG, default='/gpfs/home/cxs1031/src/freebayes/scripts/', help = 'parallel freebayes directory')
parser.add_argument('--freebayes', default='freebayes', help = 'sequential freebayes program path')
parser.add_argument('-g', '--whole_genome', help='activate whole genome analysis, use when you have multi chromosome', action='store_true')
args = parser.parse_args()
def error():
parser.print_help()
sys.exit()
def main():
if len(sys.argv) == 1:
parser.print_help()
sys.exit()
print args
scriptPath = sys.path[0]
#check that there is no blank in all file path and file name
if " " in args.reference or " " in args.pair_end:
print ("\nError: file path and file name should not contian blank space\n")
error()
#check if workspace is empty
if not os.path.exists(args.workspace):
os.makedirs(args.workspace)
if not check_command(args.python):
print("\nError: python: " + args.python + " not found\n")
error()
if not check_command(args.samtools):
print("\nError: samtools: " + args.samtools + " not found\n")
error()
print args.thread
if args.thread > 1:
#print args.thread, os.environ['MALLOC_ARENA_MAX']
if int(args.thread) > int(os.environ['MALLOC_ARENA_MAX']):
print ('\nError: detect only '+ os.environ['MALLOC_ARENA_MAX'] + ' threads available, but thread setting is ' + str(args.thread) + '\n')
print ('\tPlease set thread number not greater than available number, or reset environment variable MALLOC_ARENA_MAX\n')
error()
#exit()
if args.thread > 1 and not os.path.isdir(args.parallel_freebayes):
if args.parallel_freebayes == "/gpfs/home/cxs1031/src/freebayes/scripts/":
print ("\nError: parallel_freebayes directory not set\n")
error()
else:
print ("\nError: parallel_freebayes director: " + args.parallel_freebayes + " not exist\n")
error()
genomeList=['1','2','3','4','5','6','7','8','9','10','11','12','13','14','15','16','17','18','19','20','21','22','X','Y']
#if os.listdir(args.workspace) != []:
# print ("\nError: workspace should be empty\n")
# parser.print_help()
# sys.exit()
# create fold for temp files
for i in range(args.iteration):
print ("running iteration " + str(i+1) + ": " + str(datetime.now()))
iterFold = args.workspace + "/" + str(i+1)
referenceFile = ""
if i == 0:
referenceFile = args.reference
else:
referenceFile = args.workspace + "/" + str(i)+"/"+str(i)+".fa"
#shell_run("mkdir " + iterFold)
if not os.path.exists(iterFold):
os.makedirs(iterFold)
#check ref.fa.fai
refFai = referenceFile+".fai"
if not os.path.isfile(refFai):
faidxCommand = args.samtools + " faidx " + referenceFile
shell_run(faidxCommand)
#subprocess.call(faidxCommand, shell=True)
sortPrefix = iterFold + "/" + str(i+1) + "_sort"
if not args.e:
#run bwa
if not os.path.isfile(referenceFile+".bwt"):
indexFastaCommand = args.bwa + " index " + referenceFile
shell_run(indexFastaCommand)
#subprocess.call(indexFastaCommand, shell=True)
bwaThread = ""
if args.thread > 1:
bwaThread = " -t " + str(args.thread)
#bwaThread = " -t 4"
if i == 0 and not check_command(args.bwa):
print ("\nError: bwa command: " + args.bwa + " not found. You can set by --bwa parameter.\n")
error()
bwaCommand = args.bwa + " mem" + bwaThread + " " + referenceFile + " " + args.pair_end[0] + " " + args.pair_end[1] + " | " + args.samtools + " view -Shu - | " + args.samtools + " sort - " + sortPrefix
#bwaCommand = args.bwa + " mem" + bwaThread + " " + referenceFile + " " + args.pair_end[0] + " " + args.pair_end[1] + " | " + args.samtools + " view -Shu - > "+ iterFold + "/" + str(i+1) + ".bam"
#| " + args.samtools + " sort - " + sortPrefix
shell_run(bwaCommand)
#sortCommand = args.samtools + " sort -@ " + str(args.thread) + " " + iterFold + "/" + str(i+1) + ".bam " + sortPrefix
#shell_run(sortCommand)
else:
# run bowtie instead of bwa
samFile = iterFold + "/" + str(i+1) + ".sam"
bowtieIndexFile = referenceFile+"_bowtie2"
bowtieIndexCommand = args.bindex + " " + referenceFile + " " + bowtieIndexFile
if not os.path.isfile(bowtieIndexFile):
shell_run(bowtieIndexCommand)
bowtieCommand = args.bowtie + " -p " + str(args.thread) + " -x " + bowtieIndexFile + " -1 " + args.pair_end[0] + " -2 " + args.pair_end[1] + " -S " + samFile
shell_run(bowtieCommand)
#subprocess.call(bwaCommand, shell=True)
bamFile = iterFold + "/" + str(i+1) + ".bam"
sam2bamCommand = args.samtools + " view -Sb " + samFile + " > " + bamFile
shell_run(sam2bamCommand)
#subprocess.call(sam2bamCommand, shell=True)
sortBamCommand = args.samtools + " sort " + bamFile + " " + sortPrefix
shell_run(sortBamCommand)
#subprocess.call(sortBamCommand, shell=True)
sortBam = sortPrefix + ".bam"
indexBamCommand = args.samtools + " index " + sortBam
shell_run(indexBamCommand)
#subprocess.call(indexBamCommand, shell=True)
regionFile = args.workspace + "/" + str(i+1) + "/region_file"
regionCommand = args.python + " " + args.parallel_freebayes + "/fasta_generate_regions.py " + refFai + " 100000 > " + regionFile
vcfFile = args.workspace + "/" + str(i+1) + "/" + str(i+1) + ".vcf"
parallelFreebayesCommand = args.parallel_freebayes + "/freebayes-parallel " + regionFile + " " + str(args.thread) + " -f " + referenceFile + " " + sortBam + " > " + vcfFile
sequentialFreebayesCommand = args.freebayes + " -f " + referenceFile + " " + sortBam + " > " + vcfFile
if args.thread > 1:
shell_run(regionCommand)
#subprocess.call(regionCommand, shell=True)
shell_run(parallelFreebayesCommand)
#subprocess.call(parallelFreebayesCommand, shell=True)
else:
if not check_command(args.freebayes):
print ("\nError: freebayes: " + args.freebayes + " not found\n")
error()
shell_run(sequentialFreebayesCommand)
#subprocess.call(sequentialFreebayesCommand, shell=True)
fastaFile = iterFold + "/" + str(i+1)+".fa"
highConfidentFile = iterFold + "/" + str(i+1) + '_high_confident_on_'+str(i)+'.vcf'
lowConfidentFile = iterFold + "/" + str(i+1) + '_low_confident_on_'+str(i)+'.vcf'
if i == 0 and not os.path.isfile(scriptPath+"/modify_genome_with_small_variants"):
print ("\nError: modify_genome_with_small_variants not found\n")
error()
if not args.whole_genome:
constructCommand = scriptPath + "/modify_genome_with_small_variants -r " + referenceFile + " -s " + vcfFile + " -d " + fastaFile + " -h " + highConfidentFile + " -w " + lowConfidentFile
shell_run(constructCommand)
#subprocess.call(constructCommand, shell=True)
recover_creating_command = args.python + ' ' + scriptPath + '/create_recover_position.py ' + iterFold + '/' + str(i+1) + '_high_confident_on_'+str(i)+'.vcf > ' + iterFold + '/' + str(i+1) + '_to_' + str(i)
shell_run(recover_creating_command)
if i > 0:
for target in range(i,0,-1):
previous_iter_fold = args.workspace + "/" + str(target)
recovering_command = args.python + ' ' + scriptPath + '/recover_coordinate_donor2ref.py -v ' + iterFold + '/' + str(i+1) + '_high_confident_on_' + str(target) + '.vcf -r '+ previous_iter_fold + '/' + str(target) + '_to_' + str(target-1) + ' -f ' + iterFold + '/' +str(i+1) + '_high_confident_on_' + str(target-1) + '.vcf'
shell_run(recovering_command)
else:
if RUN:
#split ref file
genomeList = []
REF = open(referenceFile)
splitREF = [None for x in range(24)]
fileIter = -1
for line in REF.readlines():
if line.startswith(">"):
fileIter += 1
if fileIter > 0:
splitREF[fileIter-1].close()
line = line.strip()
columns = line.split(">")
filename = iterFold + "/ref_" + columns[1] + ".fa"
genomeList.append(columns[1].split('chr')[1])
splitREF[fileIter] = open(filename, "w")
splitREF[fileIter].write(">" + columns[1] + "\n")
continue
splitREF[fileIter].write(line)
if fileIter < 23:
print ('\nWarning: only deal with following ' + chr(fileIter+1) + ' chromosomes\n')
print genomeList
splitREF[fileIter].close()
#print ('\nError: only one chromosome found in whole genome mode\n')
#error()
else:
splitREF[fileIter].close()
#split vcf file
splitVCF = [None for x in range(24)]
fileIter = 0
chrName_iter = {}
for g in genomeList:
chrName = "chr"+g
filename = iterFold + "/" + chrName + '_' + str(i+1) + '_on_' + str(i) + ".vcf"
splitVCF[fileIter] = open(filename, "w")
chrName_iter[chrName] = fileIter
fileIter += 1
VCF = open(vcfFile)
vcfHead = ""
writeHead = False
for line in VCF.readlines():
if line.startswith("#"):
vcfHead += line
continue
if not writeHead:
for j in range(fileIter):
splitVCF[j].write(vcfHead)
writeHead = True
columns = line.split("\t")
chrName = columns[0]
splitVCF[chrName_iter[chrName]].write(line)
for j in range(fileIter):
splitVCF[j].close()
pool = Pool(processes=args.thread)
#construct donor genome
print ("parallel constructing chromosomes...\n")
for g in genomeList:
single_command_list = []
singleRef = iterFold + "/ref_chr" + g + ".fa"
#singleVcf = iterFold + "/chr"+g+".vcf"
singleVcf = iterFold + '/chr' + g + '_' + str(i+1) + '_on_' + str(i) + '.vcf'
singleDonor = iterFold + "/donor_chr"+g+".fa"
#singleHigh = iterFold + "/high_chr"+g+".vcf"
singleHigh = iterFold + '/chr' + g + '_' + str(i+1) + '_high_confident_on_' + str(i) + '.vcf'
#singleLow = iterFold + "/low_chr"+g+".vcf"
singleLow = iterFold + '/chr' + g + '_' + str(i+1) + '_low_confident_on_' + str(i) + '.vcf'
constructCommand = scriptPath + "/modify_genome_with_small_variants -r " + singleRef + " -s " + singleVcf + " -d " + singleDonor + " -h " + singleHigh + " -w " + singleLow
single_command_list.append(constructCommand)
recover_creating_command = args.python + ' ' + scriptPath + '/create_recover_position.py ' + singleHigh + '> ' + iterFold + '/chr' + g + '_' + str(i+1) + '_to_' + str(i)
single_command_list.append(recover_creating_command)
#shell_run(recover_creating_command)
if i > 0:
for target in range(i,0,-1):
previous_iter_fold = args.workspace + "/" + str(target)
recovering_all_command = args.python + ' ' + scriptPath + '/recover_coordinate_donor2ref.py -v ' + singleVcf + ' -r '+ previous_iter_fold + '/chr' + g + '_' + str(target) + '_to_' + str(target-1) + ' -f ' + iterFold + '/chr' + g + '_' + str(i+1) + '_on_' + str(target-1) + '.vcf'
recovering_confident_command = args.python + ' ' + scriptPath + '/recover_coordinate_donor2ref.py -v ' + singleHigh + ' -r '+ previous_iter_fold + '/chr' + g + '_' + str(target) + '_to_' + str(target-1) + ' -f ' + iterFold + '/chr' + g + '_' + str(i+1) + '_high_confident_on_' + str(target-1) + '.vcf'
single_command_list.append(recovering_all_command)
single_command_list.append(recovering_confident_command)
pool.apply_async(serial_exe, (single_command_list, ))
#shell_run(constructCommandt
pool.close()
pool.join()
print ("finish constructing new chromosomes.\n")
# combine donor genome
combineCommand = "cat " + iterFold + "/donor_chr* > " + fastaFile
shell_run(combineCommand)
#delCommand = "rm " + iterFold + "/donor_chr*"
#shell_run(delCommand)
#delCommand = "rm " + iterFold + "/ref_chr*"
#shell_run(delCommand)
if __name__ == '__main__':
main()