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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(1)
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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( '<li><a href="%s"><img src="%s" alt="" height="80" width="80">%s</a></li>\n' % ( fname, fname , fname ) )
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18 html_out.write( '</ul>\n</body>\n</html>\n' )
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19
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20 def __main__():
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21 #Parse Command Line
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22 parser = optparse.OptionParser()
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23
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24 # wrapper options
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25 parser.add_option('', '--r-script', dest='r_script', help='R script')
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26 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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27
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28 (options, args) = parser.parse_args()
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29
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30 (html_filename, html_dir) = options.html_report_from_directory
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31
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32 # Make html report directory for output.
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33 os.mkdir( html_dir )
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34
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35 # Make a tmp dir
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36 tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
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37
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38 # Build command.
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39 cmd = ( "Rscript --vanilla %s" % options.r_script )
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40
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41 # Debugging.
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42 # print cmd
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43
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44 #liubo added, for test, look at the generated R script
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45 # shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
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46
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47
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48 # Run command.
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49 try:
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50 tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
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51 tmp_stderr = open( tmp_name, 'wb' )
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52 proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
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53 returncode = proc.wait()
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54 tmp_stderr.close()
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55
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56 # Get stderr, allowing for case where it's very large.
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57 tmp_stderr = open( tmp_name, 'rb' )
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58 stderr = ''
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59 buffsize = 1048576
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60 try:
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61 while True:
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62 stderr += tmp_stderr.read( buffsize )
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63 if not stderr or len( stderr ) % buffsize != 0:
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64 break
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65 except OverflowError:
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66 pass
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67 tmp_stderr.close()
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68
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69 # Error checking.
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70 if returncode != 0:
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71 raise Exception, stderr
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72 except Exception, e:
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73 stop_err( 'Error running R script. ' + str( e ) )
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74
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75 # write the html report
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76 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
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77
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78 # Clean up temp dirs
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79 if os.path.exists( tmp_dir ):
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80 shutil.rmtree( tmp_dir )
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81
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82 if __name__=="__main__": __main__()
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