--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/restrictFromSize.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,94 @@
+#! /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.
+#
+"""Get the size distribution of a Fasta / BED file"""
+
+import os
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import *
+from commons.core.parsing.FastqParser import *
+from SMART.Java.Python.structure.TranscriptContainer import *
+from commons.core.writer.TranscriptWriter import *
+from commons.core.writer.FastaWriter 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 Size v1.0.1: Select the elements of a list of sequences or transcripts with a given size. [Category: Data Selection]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                     type="string", help="input file [compulsory] [format: file in transcript or sequence format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",                     type="string", help="format of the input [compulsory] [format: sequence or transcript file format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in transcript or sequence format given by -f]")
+    parser.add_option("-m", "--minSize",   dest="minSize",        action="store",      default=None,  type="int",    help="minimum size [format: int]")
+    parser.add_option("-M", "--maxSize",   dest="maxSize",        action="store",      default=None,  type="int",    help="maximum size [format: int]")
+    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()
+
+    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:
+        parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+        writer = TranscriptWriter(options.outputFileName, options.format, options.verbosity)
+
+
+    # treat items
+    nbItems  = parser.getNbItems()
+    progress = Progress(nbItems, "Analyzing sequences of %s" % (options.inputFileName), options.verbosity)
+    nbKept   = 0
+    nbRead   = 0
+    nbClKept = 0
+    nbClRead = 0
+    for item in parser.getIterator():
+        size      = item.getSize()
+        nb        = 1 if options.format in ("fasta", "fastq") or "nbElements" not in item.getTagNames() else float(item.getTagValue("nbElements"))
+        nbRead   += nb
+        nbClRead += 1
+        if (options.minSize == None or options.minSize <= size) and (options.maxSize == None or options.maxSize >= size):
+            writer.addElement(item)
+            nbKept   += nb
+            nbClKept += 1
+        progress.inc()
+    progress.done()
+    
+    writer.write()
+
+    print "%d items,    %d kept (%.2f%%)" % (nbRead, nbKept, 0 if nbItems == 0 else float(nbKept) / nbItems * 100)
+    if nbKept != nbClKept or nbRead != nbClRead:
+        print "%d clusters, %d kept (%.2f%%)" % (nbClRead, nbClKept, 0 if nbClRead == 0 else float(nbClKept) / nbClRead * 100)