--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/trimSequence.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,102 @@
+#! /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.
+#
+"""Remove sequences with low reliability"""
+
+from optparse import OptionParser
+from commons.core.parsing.SequenceListParser import *
+from commons.core.writer.FastaWriter import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Trim Sequences v1.0.1: Remove sequences with low reliability: low occurrences and highly repeted. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",         dest="inputFileName",    action="store",                                         type="string", help="input file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-o", "--output",        dest="outputFileName", action="store",                                         type="string", help="output file [compulsory] [format: output file in FASTA format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",            action="store",            default=1,         type="int",        help="trace level [format: int]")
+    parser.add_option("-l", "--log",             dest="log",                        action="store_true", default=False,                                help="write a log file [format: bool] [default: false]")
+    (options, args) = parser.parse_args()
+
+    parser            = SequenceListParser(options.inputFileName, options.verbosity)
+    nbSequences = parser.getNbSequences()
+    progress        = Progress(nbSequences, "Parsing file %s" % (options.inputFileName), options.verbosity)
+    
+    writer = FastaWriter(options.outputFileName, options.verbosity)
+    if options.log:
+        logHandle = open("log.txt", "w")
+    
+    letters                            = ("A", "C", "G", "T")
+    nbLowComplexity            = 0
+    nbTooManyOccurrences = 0
+    
+    for sequence in parser.getIteractor():
+        halfSize                     = len(sequence.sequence) / 2
+        occurrences                = set()
+        nbOccurrences            = dict(zip(letters, [0 for letter in letters]))
+        tooManyOccurrences = False
+        good                             = True
+        
+        for char in sequence.sequence:
+            if char in letters:
+                occurrences.add(char)
+                nbOccurrences[char] += 1
+                
+            
+        if len(occurrences) < 4:
+            nbLowComplexity += 1
+            if options.log:
+                logHandle.write("Low complexity for %s\n" % (sequence.sequence))
+            good = False
+
+        if good:
+            for letter, nbOccurrence in nbOccurrences.iteritems():
+                if nbOccurrence > halfSize:
+                    if not tooManyOccurrences:
+                        nbTooManyOccurrences += 1
+                        if options.log:
+                            logHandle.write("Too many occurrences for %s\n" % (sequence.sequence))
+                    tooManyOccurrences = True
+                    good = False
+            
+        if good:
+            writer.addSequence(sequence)
+                    
+        progress.inc()
+    progress.done()
+    
+    if options.log:
+        logHandle.close()
+        
+    print "%d out of %d have low complexity (%f%%)"             % (nbLowComplexity, nbSequences, (float(nbLowComplexity) / nbSequences * 100))        
+    print "%d out of %d have too many occurrences (%f%%)" % (nbTooManyOccurrences, nbSequences, (float(nbTooManyOccurrences) / nbSequences * 100))