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1 import sys, tempfile, subprocess, glob
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2 import os, re, shutil
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3 import 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
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8 Created by Cyril Monjeaud
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9 Cyril.Monjeaud@irisa.fr
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10
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11 WARNING :
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12
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13 TakeABreak_wrapper.py needs:
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14
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15 - dbgh5 & TakeABreak binaries in your $PATH
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16
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17 All these files are available after compiling the sources of TakeABreak :
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18
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19 http://colibread.inria.fr/files/2014/01/TakeABreak-1.1.0-Source.tar_.gz
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20
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21 or with the package_takeabreak dependency in the toolshed
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22
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23 """
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24
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25 def __main__():
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26
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27 # create a special dir inside job working dir
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28 tmp_dir = tempfile.mkdtemp()
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29 os.chdir(tmp_dir)
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30
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31 # retrieve arguments
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32 parser = optparse.OptionParser()
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33 parser.add_option("-i", dest="reads_files")
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34 parser.add_option("-k", dest="kmer")
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35 parser.add_option("-S", dest="kmersolid")
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36
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37 parser.add_option("-g", dest="graph_file")
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38 parser.add_option("-c", dest="complexity")
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39 parser.add_option("-m", dest="maxsimprct")
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40 parser.add_option("-r", dest="optimization")
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41
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42 parser.add_option("--output_graph")
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43 parser.add_option("--output_fasta")
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44 parser.add_option("--output_log")
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45
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46 (options, args) = parser.parse_args()
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47
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48 cmd_line=[]
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49 if options.reads_files:
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50 # start the command line
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51 cmd_line.append("TakeABreak")
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52 cmd_line.extend(["-in",options.reads_files,"-kmer-size",options.kmer,"-abundance",options.kmersolid])
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53 else:
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54 # start the command line
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55 os.symlink(options.graph_file, "graph.h5")
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56 cmd_line.append("TakeABreak")
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57 cmd_line.extend(["-graph", "graph.h5"])
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58
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59 cmd_line.extend(["-out","galaxy","-lct",options.complexity,"-max-sim",options.maxsimprct,"-repeat",options.optimization])
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60
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61 # execute command line
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62 p=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 = p.communicate()
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66
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67 # log file
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68 logfile=open(options.output_log, "w")
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69 logfile.write("[COMMAND LINE]"+' '.join(cmd_line)+"\n\n")
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70 logfile.write(stdoutput)
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71 logfile.write(stderror)
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72 logfile.close()
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73
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74 if options.reads_files:
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75
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76 # create output h5
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77 shutil.copy("galaxy.h5", options.output_graph)
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78
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79 # create output fasta
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80 shutil.copy("galaxy.fasta", options.output_fasta)
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81
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82 if __name__ == "__main__": __main__()
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83
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