--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/restrictFromNucleotides.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,78 @@
+#! /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 all dirty sequences"""
+
+import os
+import sys
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import *
+from commons.core.writer.FastaWriter import *
+from commons.core.parsing.FastqParser import *
+from commons.core.writer.FastqWriter import *
+from SMART.Java.Python.misc.Progress import *
+from SMART.Java.Python.misc.RPlotter import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Restrict from nucleotide v1.0.1: Remove the sequences with ambiguous nucleotides. [Category: Personal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",         dest="inputFileName",    action="store",                                                type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
+    parser.add_option("-f", "--format",        dest="inputFileName",    action="store",            default="fasta",    type="string", help="format of the input and output files [compulsory] [format: sequence file format]")
+    parser.add_option("-o", "--output",        dest="outputFileName", action="store",                                                type="string", help="output file [compulsory] [format: output file in sequence format given by -f]")
+    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()
+
+    # treat items
+    if options.format == "fasta":
+        parser     = FastaParser(options.inputFileName, options.verbosity)
+        writer     = FastaWriter(options.outputFileName, options.verbosity)
+    elif options.format == "fastq":
+        parser     = FastqParser(options.inputFileName, options.verbosity)
+        writer     = FastqWriter(options.outputFileName, options.verbosity)
+    else:
+        sys.exit("Do not understand '%s' format." % (options.format))
+    nbSequences = parser.getNbSequences()
+    print "sequences: %d" % (nbSequences)
+    
+    progress = Progress(nbSequences, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
+    nbKept     = 0
+    for sequence in parser.getIterator():
+        if not sequence.containsAmbiguousNucleotides():
+            writer.addSequence(sequence)
+            nbKept += 1
+        progress.inc()
+    progress.done()
+
+    print "%d items, %d kept (%.2f%%)" % (nbSequences, nbKept, float(nbKept) / nbSequences * 100)