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1 #!/usr/bin/python
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2 #-*- coding: utf-8 -*-
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3 #Libraries:
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4 import os, os.path, argparse, sys, gzip, re
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5
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6
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7
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8 ##### MAIN
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9 def __main__():
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10 ### Arguments:
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11 parser = argparse.ArgumentParser(description='''Launch Ssuis_serotypingPipeline.pl with correct argument''', epilog="""This script needs few options use -h to see it.""")
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12
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13 parser.add_argument('--fastq_file', dest='ffile')
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14 parser.add_argument('--scoreName', dest='sname')
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15 parser.add_argument('--output2', dest='o2')
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16 parser.add_argument('--output3', dest='o3')
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17 parser.add_argument('--output4', dest='o4')
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18 parser.add_argument('--output5', dest='o5')
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19 parser.add_argument('--output6', dest='o6')
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20 parser.add_argument('--output7', dest='o7')
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21 parser.add_argument('--output8', dest='o8')
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22 parser.add_argument('--serotype_db', dest='sd')
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23 parser.add_argument('--serotype_definitions', dest='sdef')
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24 parser.add_argument('--cps2K', dest='cps')
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25 parser.add_argument('--Virulence_db', dest='Vdb')
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26 parser.add_argument('--recN_db', dest='recdb')
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27 parser.add_argument('--MLST_definitions', dest='MLSTdef')
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28 parser.add_argument('--MLST_db', dest='MLSTdb')
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29 parser.add_argument('--ends', dest='ends')
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30 parser.add_argument('--forward', dest='f')
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31 parser.add_argument('--reverse', dest='r')
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32
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33 ### Get argument in variable:
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34 options = parser.parse_args()
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35 ffile = options.ffile
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36 sname = options.sname
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37 output2 = options.o2
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38 output3 = options.o3
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39 output4 = options.o4
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40 output5 = options.o5
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41 output6 = options.o6
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42 output7 = options.o7
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43 output8 = options.o8
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44 sd = options.sd
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45 sdef = options.sdef
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46 cps = options.cps
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47 Vdb = options.Vdb
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48 recdb = options.recdb
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49 MLSTdef = options.MLSTdef
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50 MLSTdb = options.MLSTdb
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51 ends = options.ends
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52 f = options.f
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53 r = options.r
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54
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55 way_pipeline = "/results/anses/bin/SsuisSerotyping_pipeline/"
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56 input_path = os.path.splitext(output2)[0]+"_input_file_test/"
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57 output_path = os.path.splitext(output2)[0]+"_Results/"
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58 os.system("mkdir -p "+input_path)
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59 os.system("cp "+ffile+" "+input_path+"/file_test.fastq")
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60 fdir = input_path
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61
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62 if ends == "se":
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63 f = "SINGLE"
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64 r = "SINGLE"
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65
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66 if sd is None:
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67 os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
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68 else:
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69 os.system("perl "+way_pipeline+"/Ssuis_serotypingPipeline.pl --fastq_directory "+str(fdir)+" --scoreName "+output_path+"Results --serotype_db "+str(sd)+" --serotype_definitions "+str(sdef)+" --cps2K "+str(cps)+" --Virulence_db "+str(Vdb)+" --recN_db "+str(recdb)+" --MLST_definitions "+str(MLSTdef)+" --MLST_db "+str(MLSTdb)+" --ends "+str(ends)+" --forward "+str(f)+" --reverse "+str(r))
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70
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71 os.system("rm -r "+fdir)
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72 os.system("mv "+output_path+"/Results_FinalResults.txt "+sname)
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73 os.system("mv "+output_path+"/Results_MLSTResults.txt "+output2)
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74 os.system("mv "+output_path+"/Results_recN__fullgenes__recN_full__results.txt "+output3)
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75 os.system("mv "+output_path+"/Results_speciesConfirmation.txt "+output4)
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76 os.system("mv "+output_path+"/Results_FinalSerotypingResults.txt "+output5)
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77 os.system("mv "+output_path+"/Results_InitialCapsuleResults.txt "+output6)
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78 os.system("mv "+output_path+"/Results_VirulenceFactors__fullgenes__Virulence__results.txt "+output7)
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79 os.system("mv "+output_path+"/Results_VirulenceFactorResults.txt "+output8)
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80 #### MAIN END
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81 if __name__ == "__main__": __main__()
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82
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