Mercurial > repos > cstrittmatter > seqsero_v2

annotate SeqSero2.py @ 0:6275272ebcbc draft

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author cstrittmatter
date Thu, 21 Dec 2017 12:45:31 -0500
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1 #!/usr/bin/env python
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2
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3 ############################################################################
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4 # Copyright (c) 2014-2015 University of Georgia
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5 # Developer: Shaokang Zhang, zskzsk@uga.edu
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6 # All Rights Reserved
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7 ############################################################################
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8
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9 import argparse,os,sys,time,random
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10
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11 def main():
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12 parser = argparse.ArgumentParser(usage='SeqSero2.py -i <input_data> [-p <number of threads>] [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com')#add "-m <data_type>" in future
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13 parser.add_argument("-i",nargs="+", help="<string>: path/to/input_data")
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14 parser.add_argument("-b",choices=['sam','mem'],default="mem",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem),default=mem")
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15 parser.add_argument("-p",default="1",help="<int>: if p>4, only 4 threads will be used for assembly, default=1")
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16 args=parser.parse_args()
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17 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
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18 if len(sys.argv)==1:
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19 os.system(dirpath+"/SeqSero2.py -h")
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20 else:
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21 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
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22 request_id += str(random.randint(1, 10000000))
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23 make_dir="SeqSero_result_"+request_id
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24 os.system("mkdir "+make_dir)
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25 os.system("cp -rf "+dirpath+"/database/H_and_O_and_specific_genes.fasta "+make_dir)
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26 #mode_choice=args.m
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27 mapping_mode=args.b
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28 threads=args.p
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29 dataset=args.i
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30 os.system("cp "+dataset[0]+" "+make_dir)
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31 # print len(dataset)
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32 os.system("cp "+dataset[1]+" "+make_dir)
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33 fnameA=dataset[0].split("/")[-1]
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34 fnameB=dataset[1].split("/")[-1]
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35 os.chdir(make_dir)
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36 os.system("python2.7 "+dirpath+"/libs/mapping_and_assembly_hybrid.py H_and_O_and_specific_genes.fasta "+mapping_mode+" "+str(threads)+" "+fnameA+" "+fnameB)
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37 os.system("rm H_and_O_and_specific_genes.fasta* *.bam *.sam *.fastq *.fastq.gz *.fq temp.txt *.xml "+fnameA+"*_db* 2> /dev/null")
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38 print "Output_directory:",make_dir
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39 #print "\n\n\nResult:\n"
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40 #os.system("cat Seqsero_result.txt")
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41
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42 if __name__ == '__main__':
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43 main()