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1 #!/usr/bin/env python
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2
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3 import sys, subprocess, tempfile, shutil, os.path
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4
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5 def get_top_count( filename ):
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6 for line in open( filename ):
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7 if line.startswith( 'outputNum' ):
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8 return int( line.split()[-1].strip() )
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9
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10 def stop_err( tmp_dir, exception ):
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11 print >> sys.stderr, "Error running CCAT."
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12 shutil.rmtree( tmp_dir ) #some error has occurred, provide info and remove possibly non-empty temp directory
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13 raise exception
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14
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15 def main():
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16 CCAT_BINARY = "/usr/bin/ccat/CCAT3.0/bin/CCAT"
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17 input_tag_file = sys.argv[1]
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18 input_control_file = sys.argv[2]
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19 genome = sys.argv[3]
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20 input_config_file = sys.argv[4]
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21 project_name = sys.argv[5]
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22 output_peak_file = sys.argv[6]
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23 output_region_file = sys.argv[7]
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24 output_top_file = sys.argv[8]
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25 output_log_file = sys.argv[9]
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26 root_dir = sys.argv[10]
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27
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28 ###### CREATE ANNOTATION FILES #########
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29 databasePath = root_dir+"/database/files"
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30
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31 subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations', shell=True)
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32 subprocess.Popen('mkdir -p '+databasePath+'/nebulaAnnotations/'+genome, shell=True)
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33
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34 nebulaGenomePath=databasePath+"/nebulaAnnotations/"+genome
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35
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36 FAIFILE='n'
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37 LENFILE='n'
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38 DICTFILE='n'
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39 CHROFILE='n'
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40 MAPFILE='n'
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41
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42 if not os.path.isfile(nebulaGenomePath+"/"+genome+".len"):
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43 FAIFILE='y'
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44 LENFILE='y'
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45
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46 FILEPATH=databasePath.replace("database/files","tool-data")
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47
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48 cmd='bash /usr/bin/create_annotation_files.sh '+FAIFILE+" "+LENFILE+" "+DICTFILE+" "+CHROFILE+" "+FILEPATH+" "+genome+" "+MAPFILE+" "+nebulaGenomePath
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49 process=subprocess.Popen(cmd, shell=True)
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50 process.wait()
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51
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52 chrom_info_file=nebulaGenomePath+"/"+genome+".len"
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53
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54 tmp_dir = tempfile.mkdtemp()
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55 try:
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56 proc = subprocess.Popen( args="%s %s > %s" % ( CCAT_BINARY, " ".join( map( lambda x: "%s" % x, [ input_tag_file, input_control_file, chrom_info_file, input_config_file, project_name ] ) ), output_log_file ), shell=True, cwd=tmp_dir )
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57 proc.wait()
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58 if proc.returncode:
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59 raise Exception( "Error code: %i" % proc.returncode )
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60 output_num = get_top_count( input_config_file )
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61 shutil.move( os.path.join( tmp_dir, "%s.significant.peak" % project_name ), output_peak_file )
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62 shutil.move( os.path.join( tmp_dir, "%s.significant.region" % project_name ), output_region_file )
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63 shutil.move( os.path.join( tmp_dir, "%s.top%i.peak" % ( project_name, output_num ) ), output_top_file )
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64 except Exception, e:
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65 return stop_err( tmp_dir, e )
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66 os.rmdir( tmp_dir ) #clean up empty temp working directory
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67
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68 if __name__ == "__main__": main()
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