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1 #!/usr/bin/env python2.6
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2 import subprocess
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3 import sys
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4 import re
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5 import shutil
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6 import os
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7 from optparse import OptionParser
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8
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9 toolname = "MRF"
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10
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11
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12 def main():
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13
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14 tool_path = os.path.dirname(os.path.realpath(sys.argv[0])) + "/" + toolname
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15
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16 usage = "usage: %prog [options] arg"
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17 parser = OptionParser(usage)
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18 parser.add_option("-f", "--file",
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19 action="store", type="string", dest="configfile",
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20 help="File containing the Values")
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21
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22 parser.add_option("-o", "--output",
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23 action="store", type="string", dest="outputfile", nargs=4,
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24 help="Output file where to store the result")
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25
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26 (options, args) = parser.parse_args()
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27
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28 if options.configfile is None or options.outputfile is None:
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29 print "Missing arguments"
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30 parser.print_help()
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31 exit (1)
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32
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33 mrf(tool_path, options.configfile, options.outputfile)
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34
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35 def mrf(tool_path, configfile, outputfile):
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36
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37
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38 f = open(configfile, 'r+b')
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39
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40 tool = subprocess.Popen([tool_path],stdin=f, stdout=subprocess.PIPE)
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41 tool.wait()
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42 f.close()
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43
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44 if tool.returncode != 0:
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45 sys.stderr.write("There was a problem when running the $toolname tool")
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46 output = tool.stdout.read()
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47 print output
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48 exit (1)
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49
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50 output = tool.stdout.read()
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51 print output
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52
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53 # Determining the Output file generated by MRF
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54 m1 = re.search("(.*Cluster: )*(\/.*\.pos$)", output, re.MULTILINE )
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55 m1_1 = re.search("(\/.*\/dataset_[0-9]*.dat-dataset_[0-9]*\.dat-\w*)(\..*)", m1.group(2), re.MULTILINE)
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56 prefix = m1_1.group(1)
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57
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58 m2 = re.search("(.*Cluster: )*(\/.*\.pos$)", output, re.MULTILINE )
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59 file1 = m2.group(2)
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60
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61 file2 = prefix + '.mrf.txt'
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62
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63 m3 = re.search("(.*Morphology: )*(\/.*\.txt$)",output, re.MULTILINE )
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64 file3 = m3.group(2)
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65
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66 file4 = prefix + '.wc_histogram.txt'
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67
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68 #Move the generated files to the Galaxy outputs and remove the tmp file
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69
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70 shutil.move(file1, outputfile[0])
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71
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72 lines = open(file2).readlines()
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73 open(outputfile[1], 'w').writelines(lines[1:])
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74 os.remove(file2)
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75
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76 shutil.move(file3, outputfile[2])
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77 shutil.move(file4, outputfile[3])
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78
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79 if __name__ == "__main__":
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80 main()
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