--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/updateQual.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,86 @@
+#! /usr/bin/env python
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# This software is governed by the CeCILL license under French law and
+# abiding by the rules of distribution of free software. You can use,
+# modify and/ or redistribute the software under the terms of the CeCILL
+# license as circulated by CEA, CNRS and INRIA at the following URL
+# "http://www.cecill.info".
+# 
+# As a counterpart to the access to the source code and rights to copy,
+# modify and redistribute granted by the license, users are provided only
+# with a limited warranty and the software's author, the holder of the
+# economic rights, and the successive licensors have only limited
+# liability.
+# 
+# In this respect, the user's attention is drawn to the risks associated
+# with loading, using, modifying and/or developing or reproducing the
+# software by the user in light of its specific status of free software,
+# that may mean that it is complicated to manipulate, and that also
+# therefore means that it is reserved for developers and experienced
+# professionals having in-depth computer knowledge. Users are therefore
+# encouraged to load and test the software's suitability as regards their
+# requirements in conditions enabling the security of their systems and/or
+# data to be ensured and, more generally, to use and operate it in the
+# same conditions as regards security.
+# 
+# The fact that you are presently reading this means that you have had
+# knowledge of the CeCILL license and that you accept its terms.
+#
+"""Update a .qual file given a .fasta file"""
+
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Update Qual v1.0.1: Remove the sequence in a Qual file which are not in the corresponding Fasta file. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-f", "--fasta",         dest="fastaFile",    action="store",                                         type="string", help="fasta file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-q", "--qual",            dest="qualFile",     action="store",                                         type="string", help="qual file [compulsory] [format: file in QUAL format]")
+    parser.add_option("-o", "--output",        dest="outputFile", action="store",                                         type="string", help="output file [compulsory] [format: output file in QUAL format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",    action="store",            default=1,         type="int",        help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    parser             = SequenceListParser(options.fastaFile, options.verbosity)
+    nbSequences    = parser.getNbSequences()
+    progress         = Progress(nbSequences, "Parsing file %s" % (options.fastaFile), options.verbosity)
+    qualHandle     = open(options.qualFile)
+    outputHandle = open(options.outputFile, "w")
+    nbRefused        = 0
+    nbTotal            = 0
+    
+    names = []
+    while parser.getNextSequence():
+        sequence = parser.getCurrentSequence()
+        nbTotal += 1
+    
+        found = False
+        name    = None
+        for line in qualHandle:
+            line = line.strip()
+            if line[0] == ">":
+                name = line[1:]
+                if name == sequence.name:
+                    found = True
+                else:
+                    nbRefused += 1
+            else:
+                if found:
+                    outputHandle.write(">%s\n%s\n" % (name, line))
+                    found = False
+                    name    = None
+                    break
+        progress.inc()
+    progress.done()
+
+    
+    outputHandle.close()
+    qualHandle.close()
+    
+    print "%d out of %d are refused (%f%%)"             % (nbRefused, nbTotal, (float(nbRefused) / nbTotal * 100))