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1 #!/usr/bin/env python
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2
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3 ### Runs "r_script" and generates a HTML report
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4 ### Inspired on cuffdiff_wrapper.py and gatk_wrapper.py
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5 ### Carlos Borroto <carlos.borroto@gmail.com>
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6
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7 import optparse, os, shutil, subprocess, sys, tempfile
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8
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9 def stop_err( msg ):
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10 sys.stderr.write( "%s\n" % msg )
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11 sys.exit()
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12
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13 def html_report_from_directory( html_out, dir ):
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14 html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
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15 for fname in sorted( os.listdir( dir ) ):
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16 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
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17 html_out.write( '</ul>\n</body>\n</html>\n' )
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18
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19 def __main__():
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20 #Parse Command Line
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21 parser = optparse.OptionParser()
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22
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23 # wrapper options
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24 parser.add_option('', '--r-script', dest='r_script', help='R script')
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25 parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"')
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26
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27 (options, args) = parser.parse_args()
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28
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29 (html_filename, html_dir) = options.html_report_from_directory
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30
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31 # Make html report directory for output.
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32 os.mkdir( html_dir )
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33
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34 # Make a tmp dir
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35 tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
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36
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37 # Build command.
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38 cmd = ( "Rscript --vanilla %s" % options.r_script )
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39
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40 # Debugging.
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41 print cmd
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42
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43 #liubo added, for test, look at the generated R script
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44 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
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45
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46
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47 # Run command.
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48 try:
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49 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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50 tmp_stderr = open( tmp_name, 'wb' )
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51 proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
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52 returncode = proc.wait()
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53 tmp_stderr.close()
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54
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55 # Get stderr, allowing for case where it's very large.
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56 tmp_stderr = open( tmp_name, 'rb' )
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57 stderr = ''
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58 buffsize = 1048576
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59 try:
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60 while True:
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61 stderr += tmp_stderr.read( buffsize )
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62 if not stderr or len( stderr ) % buffsize != 0:
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63 break
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64 except OverflowError:
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65 pass
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66 tmp_stderr.close()
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67
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68 # Error checking.
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69 if returncode != 0:
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70 raise Exception, stderr
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71 except Exception, e:
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72 stop_err( 'Error running R script. ' + str( e ) )
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73
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74 # write the html report
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75 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
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76
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77 # Clean up temp dirs
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78 if os.path.exists( tmp_dir ):
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79 shutil.rmtree( tmp_dir )
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80
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81 if __name__=="__main__": __main__()
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