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1 #!/usr/bin/env python
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2 import sys, subprocess, glob
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3 import os, re, shutil, optparse
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4 from os.path import basename
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5
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6 """
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7 WARNING :
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8
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9 Mapsembler2.py needs mapsembler2_exe binaries in your $PATH
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10
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11 Mapsember2 is available after compiling sources :
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12
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13 http://www.irisa.fr/symbiose/people/ppeterlongo/mapsembler2_2.2.3.zip
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14
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15 or with the galaxy_mapsembler2 package in the GenOuest toolshed
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16
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17
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18 """
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19
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20 def __main__():
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21
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22 # arguments recuperation
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23 parser = optparse.OptionParser()
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24 parser.add_option("-s", dest="input_starters")
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25 parser.add_option("-r", dest="input_files")
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26 parser.add_option("-t", dest="output_extension")
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27 parser.add_option("-k", dest="kmer")
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28 parser.add_option("-c", dest="coverage")
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29 parser.add_option("-d", dest="substitutions")
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30 parser.add_option("-g", dest="genome_size")
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31 parser.add_option("-f", dest="process_search")
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32 parser.add_option("-x", dest="max_length")
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33 parser.add_option("-y", dest="max_depth")
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34 parser.add_option("--output")
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35 parser.add_option("-i", dest="index_files")
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36
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37 (options, args) = parser.parse_args()
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38
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39 # import tools
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40 os.symlink(os.environ['TOOLS'], os.getcwd()+'/tools')
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41
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42 # execute mapsembler
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43 cmd_line=[]
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44 cmd_line.append("run_mapsembler2_pipeline.sh")
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45
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46 # change starter extension
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47 cmd_line.extend(["-s", options.input_starters])
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48
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49 #inputs
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50 cmd_line.append("-r")
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51
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52 #cmd_line.append(inputs)
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53 cmd_line.append(' '.join(options.input_files.split(",")))
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54
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55 # add parameters into the command line
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56 cmd_line.extend(["-t", options.output_extension, "-k", options.kmer, "-c", options.coverage, "-d", options.substitutions, "-g", options.genome_size, "-f", options.process_search, "-x", options.max_length, "-y", options.max_depth])
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57
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58 # open the output log file
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59 log = open(options.output, "w")
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60 log.write("[COMMAND LINE] "+' '.join(cmd_line))
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61
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62 process=subprocess.Popen(cmd_line,
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63 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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64
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65 stdoutput, stderror = process.communicate()
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66
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67 # results recuperation
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68 log.write(stdoutput)
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69 log.write(stderror)
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70
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71 # close log file
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72 log.close()
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73
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74 # move results files inside the job_outputs dir
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75 os.mkdir("job_outputs")
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76 result_files = glob.glob("res_*")
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77 for file in result_files:
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78 shutil.move(file, "job_outputs/")
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79
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80
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81 # move index files
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82 if options.index_files == "true":
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83 index_files = glob.glob("index_*")
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84 for index in index_files:
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85 shutil.move(index, "job_outputs/")
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86
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87 # move json result into gjson
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88 json_files = glob.glob("job_outputs/*.json")
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89 for json in json_files:
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90 shutil.move(json, json.replace(".json", ".gjson"))
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91
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92
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93 if __name__ == "__main__": __main__()
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94
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