--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/quake_wrapper.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,132 @@
+#!/usr/bin/python
+#
+# Copyright (c) 2011, Pacific Biosciences of California, Inc.
+#
+# All rights reserved.
+#
+#Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
+#    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+#    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+#    * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+#
+#THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+#WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY
+#DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+#LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+import sys
+import os
+import subprocess
+
+QUAKE_EXE = os.path.join( os.path.dirname(os.path.abspath(sys.argv[0])), 'quake.py' )
+cmdLine = sys.argv
+cmdLine.pop(0)
+
+#
+# horribly not robust, but it was a pain to rewrite everything with
+# optparse
+#
+j = -1
+cut = 0
+for i,arg in enumerate(cmdLine):
+    if '--default_cutoff' in arg:
+        j = i
+        cut = int(arg.split('=')[1])
+if j>=0:
+    cmdLine = cmdLine[:j] + cmdLine[j+1:]
+
+j = -1
+output=''
+for i,arg in enumerate(cmdLine):
+    if '--output' in arg:
+        j = i
+        output = arg.split('=')[1]
+if j>=0:
+    cmdLine = cmdLine[:j] + cmdLine[j+1:]
+
+def backticks( cmd, merge_stderr=True ):
+    """
+    Simulates the perl backticks (``) command with error-handling support
+    Returns ( command output as sequence of strings, error code, error message )
+    """
+    if merge_stderr:
+        _stderr = subprocess.STDOUT
+    else:
+        _stderr = subprocess.PIPE
+
+    p = subprocess.Popen( cmd, shell=True, stdin=subprocess.PIPE,
+                          stdout=subprocess.PIPE, stderr=_stderr,
+                          close_fds=True )
+
+    out = [ l[:-1] for l in p.stdout.readlines() ]
+
+    p.stdout.close()
+    if not merge_stderr:
+        p.stderr.close()
+
+    # need to allow process to terminate
+    p.wait()
+
+    errCode = p.returncode and p.returncode or 0
+    if p.returncode>0:
+        errorMessage = os.linesep.join(out)
+        output = []
+    else:
+        errorMessage = ''
+        output = out
+
+    return output, errCode, errorMessage
+
+def to_stdout():
+    def toCorFastq(f):
+        stem, ext = os.path.splitext( os.path.basename(f) )
+        dir = os.path.dirname(f)
+        corFastq = os.path.join(dir,'%s.cor%s' % (stem,ext) )
+        if not os.path.exists(corFastq):
+            print >>sys.stderr, "Can't find path %s" % corFastq
+            sys.exit(1)
+        return corFastq
+    if '-r' in cmdLine:
+        fastqFile = cmdLine[ cmdLine.index('-r')+1 ]
+        corFastq = toCorFastq(fastqFile)
+        infile = open( corFastq, 'r' )
+        for line in infile:
+            sys.stdout.write( line )
+        infile.close()
+    else:
+        fofnFile = cmdLine[ cmdLine.index('-f')+1 ]
+        infile = open(fofnFile,'r')
+        for line in infile:
+            line = line.strip()
+            if len(line)>0:
+                fastqFiles = line.split()
+                break
+        infile.close()
+        outs = output.split(',')
+        for o,f in zip(outs,fastqFiles):
+            cf = toCorFastq(f)
+            os.system( 'cp %s %s' % ( cf, o ) )
+
+def run():
+    cmd = '%s %s' % ( QUAKE_EXE, " ".join(cmdLine) )
+    output, errCode, errMsg = backticks( cmd )
+
+    if errCode==0:
+        to_stdout()
+    else:
+        # if Quake exits with an error in cutoff determination we  
+        # can force correction if requested
+        if 'cutoff.txt' in errMsg and cut>0:
+            outfile = open( 'cutoff.txt', 'w' )
+            print >>outfile, str(cut)
+            outfile.close()
+            cmd = '%s --no_count --no_cut %s' % ( QUAKE_EXE, " ".join(cmdLine) )
+            output, errCode, errMsg = backticks( cmd )
+        if errCode==0:
+            to_stdout()
+        else:
+            print >>sys.stderr, errMsg
+            sys.exit(1)
+
+if __name__=='__main__': run()