Mercurial > repos > jjohnson > cummerbund

diff cummerbund_wrapper.py @ 0:8ba5f0460b1e

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author jjohnson
date Mon, 01 Oct 2012 14:08:13 -0400
parents
children 6a9bc26ab8d9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cummerbund_wrapper.py	Mon Oct 01 14:08:13 2012 -0400
@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+
+### Runs "r_script" and generates a HTML report
+### Inspired on cuffdiff_wrapper.py and gatk_wrapper.py
+### Carlos Borroto <carlos.borroto@gmail.com>
+
+import optparse, os, shutil, subprocess, sys, tempfile
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+def html_report_from_directory( html_out, dir ):
+    html_out.write( '<html>\n<head>\n<title>Galaxy - cummeRbund Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
+    for fname in sorted( os.listdir( dir ) ):
+        html_out.write(  '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
+    html_out.write( '</ul>\n</body>\n</html>\n' )
+
+def __main__():
+    #Parse Command Line
+    parser = optparse.OptionParser()
+
+    # wrapper options
+    parser.add_option('', '--r-script', dest='r_script', help='R script')
+    parser.add_option('', '--html-report-from-directory', dest='html_report_from_directory', type="string", nargs=2, help='"Target HTML File" "Directory"')
+        
+    (options, args) = parser.parse_args()
+    
+    (html_filename, html_dir) = options.html_report_from_directory
+    
+    # Make html report directory for output.
+    os.mkdir( html_dir )
+    
+    # Make a tmp dir
+    tmp_dir = tempfile.mkdtemp( prefix='tmp-cummeRbund-' )
+    
+    # Build command.
+    cmd = ( "Rscript --vanilla %s" % options.r_script )
+    
+    # Debugging.
+    print cmd
+
+#liubo added, for test, look at the generated R script
+#    shutil.copy2(options.r_script, '/nfs/software/galaxy/r_script')
+
+    
+    # Run command.
+    try:
+        tmp_name = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
+        tmp_stderr = open( tmp_name, 'wb' )
+        proc = subprocess.Popen( args=cmd, shell=True, cwd=html_dir, stderr=tmp_stderr.fileno() )
+        returncode = proc.wait()
+        tmp_stderr.close()
+        
+        # Get stderr, allowing for case where it's very large.
+        tmp_stderr = open( tmp_name, 'rb' )
+        stderr = ''
+        buffsize = 1048576
+        try:
+            while True:
+                stderr += tmp_stderr.read( buffsize )
+                if not stderr or len( stderr ) % buffsize != 0:
+                    break
+        except OverflowError:
+            pass
+        tmp_stderr.close()
+        
+        # Error checking.
+        if returncode != 0:
+            raise Exception, stderr
+    except Exception, e:
+        stop_err( 'Error running R script. ' + str( e ) )
+    
+    # write the html report
+    html_report_from_directory( open( html_filename, 'wb' ), html_dir )
+    
+    # Clean up temp dirs
+    if os.path.exists( tmp_dir ):
+        shutil.rmtree( tmp_dir )
+
+if __name__=="__main__": __main__()