--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/restrictSequenceList.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,113 @@
+#! /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.
+#
+"""Restrict a sequence list with some names"""
+
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.WriterChooser import WriterChooser
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc import Utils
+
+class RestrictSequenceList(object):
+
+    def __init__(self, verbosity):
+        self.verbosity = verbosity
+        self.exclude   = False
+
+    def setInputFileName(self, fileName, format):
+        chooser = ParserChooser(self.verbosity)
+        chooser.findFormat(format)
+        self.parser = chooser.getParser(fileName)
+
+    def setExclusion(self, boolean):
+        self.exclude = boolean
+
+    def setOutputFileName(self, fileName, format):
+        chooser = WriterChooser(self.verbosity)
+        chooser.findFormat(format)
+        self.writer = chooser.getWriter(fileName)
+
+    def setNamesFileName(self, fileName):
+        self.namesFileName = fileName
+
+    def _readNames(self):
+        self.names = []
+        handle = open(self.namesFileName)
+        for name in handle:
+            self.names.append(name.strip())
+        handle.close()
+
+    def _write(self):
+        nbElements = self.parser.getNbItems()
+        progress   = Progress(nbElements, "Parsing input file", self.verbosity)
+        nbRead     = 0
+        nbWritten  = 0
+        for element in self.parser.getIterator():
+            name    = element.getName()
+            nbRead += 1
+            if Utils.xor(name in self.names, self.exclude):
+                self.writer.addElement(element)
+                nbWritten += 1
+            if name in self.names:
+                self.names.remove(name)
+            progress.inc()
+        progress.done()
+        if self.verbosity > 0:
+            print "%d read" % (nbRead)
+            print "%d written (%d%%)" % (nbWritten, 0 if nbRead == 0 else round(float(nbWritten) / nbRead * 100))
+    
+    def run(self):
+        self._readNames()
+        self._write()
+        if self.names:
+            print "Some names are not present in the file: %s" % ", ".join(self.names)
+        
+
+
+if __name__ == "__main__":
+    
+    description = "Restrict Sequence List v1.0.1: Keep the elements of a list of sequences whose name is mentionned in a given file. [Category: Data Selection]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFile",  action="store",                       type="string", help="input file [compulsory] [format: file in sequence format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",     action="store",      default="fasta", type="string", help="format of the input and output files [compulsory] [format: sequence file format] [default: fasta]")
+    parser.add_option("-n", "--name",      dest="names",      action="store",                       type="string", help="names of the transcripts [compulsory] [format: file in TXT format]")
+    parser.add_option("-o", "--output",    dest="outputFile", action="store",                       type="string", help="output file [format: output file in sequence format given by -f]")
+    parser.add_option("-x", "--exclude",   dest="exclude",    action="store_true", default=False,                  help="output all those whose name is NOT on the list [format: boolean]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",  action="store",      default=1,       type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    rsl = RestrictSequenceList(options.verbosity)
+    rsl.setInputFileName(options.inputFile, options.format)
+    rsl.setOutputFileName(options.outputFile, options.format)
+    rsl.setNamesFileName(options.names)
+    rsl.setExclusion(options.exclude)
+    rsl.run()