Mercurial > repos > charles_s_test > seqsero2

annotate SeqSero.py @ 7:3d6680af0bec draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 16:30:27 -0500
parents 6895de35a263
children 53efef402c51
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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 # All Rights Reserved
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6 ############################################################################
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7
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8 import argparse,os,sys,time,random
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9
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10 def main():
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11 parser = argparse.ArgumentParser(usage='SeqSero.py -m <data_type> -i <input_data> [-b <BWA_algorithm>]\n\nDevelopper: Shaokang Zhang (zskzsk@uga.edu) and Xiangyu Deng (xdeng@uga.edu)\n\nContact email:seqsero@gmail.com')
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12 parser.add_argument("-m", choices=['1','2','3', '4'],help="<int>: '1'(pair-end reads, interleaved),'2'(pair-end reads, seperated),'3'(single-end reads), '4'(assembly)")
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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="sam",help="<string>: 'sam'(bwa samse/sampe), 'mem'(bwa mem), default=sam")
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15 args=parser.parse_args()
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16 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))
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17 if len(sys.argv)==1:
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18 os.system(dirpath+"/SeqSero.py -h")
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19 else:
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20 request_id = time.strftime("%m_%d_%Y_%H_%M_%S", time.localtime())
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21 request_id += str(random.randint(1, 10000000))
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22 make_dir="SeqSero_result_"+request_id
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23 os.system("mkdir "+make_dir)
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24 os.system("cp -rf "+dirpath+"/database "+make_dir)
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25 mode_choice=args.m
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26 mapping_mode=args.b
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27 dataset=args.i
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28 if mode_choice=="1":
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29 print(dataset[0])
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30 os.system("cp "+dataset[0]+" "+make_dir)
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31 os.chdir(make_dir)
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32 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1")
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33 print("\n\n\nResult:\n")
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34 os.system("cat Seqsero_result.txt")
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35 os.system("rm "+dataset[0].split("/")[-1])
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36 elif mode_choice=="2":
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37 os.system("cp "+dataset[0]+" "+make_dir)
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38 os.system("cp "+dataset[1]+" "+make_dir)
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39 fnameA=dataset[0].split("/")[-1]
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40 fnameB=dataset[1].split("/")[-1]
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41 os.chdir(make_dir)
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42 print("check fastq id and make them in accordance with each other...please wait...")
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43 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2")
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44 print("\n\n\nResult:\n")
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45 os.system("cat Seqsero_result.txt")
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46 elif mode_choice=="3":
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47 os.system("cp "+dataset[0]+" "+make_dir)
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48 os.chdir(make_dir)
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49 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3")
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50 print("\n\n\nResult:\n")
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51 os.system("cat Seqsero_result.txt")
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52 elif mode_choice=="4":
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53 os.system("cp "+dataset[0]+" "+make_dir)
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54 os.chdir(make_dir)
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55 os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1])
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56 print("\n\n\nResult:\n")
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57 os.system("cat Seqsero_result.txt")
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58
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59 if __name__ == '__main__':
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60 main()