--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/trimAdaptor.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,107 @@
+#! /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.
+#
+"""Trim the sequences from a 5' adaptor"""
+
+import sys
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import FastaParser
+from commons.core.parsing.FastqParser import FastqParser
+from commons.core.writer.FastaWriter import FastaWriter
+from commons.core.writer.FastqWriter import FastqWriter
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc import Utils
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Trim Adaptor v1.0.1: Remove the 3' adaptor of a list of reads. [Category: Data Modification]"
+
+    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="format",         action="store",               type="string", help="format of file [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("-a", "--adaptor",   dest="adaptor",        action="store",               type="string", help="adaptor [compulsory] [format: string]")
+    parser.add_option("-e", "--errors",    dest="errors",         action="store", default=0,    type="int" ,   help="number of errors in percent [format: int] [default: 0]")
+    parser.add_option("-n", "--noAdaptor", dest="noAdaptor",      action="store", default=None, type="string", help="file name where to print sequences with no adaptor [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]")
+    (options, args) = parser.parse_args()
+
+    minSize = 2
+
+    if options.format == "fasta":
+        parser = FastaParser(options.inputFileName, options.verbosity)
+    elif options.format == "fastq":
+        parser = FastqParser(options.inputFileName, options.verbosity)
+    else:
+        sys.exit("Cannot handle files with '%s' format." % (options.format))
+
+    if options.format == "fasta":
+        writer = FastaWriter(options.outputFileName, options.verbosity)
+    elif options.format == "fastq":
+        writer = FastqWriter(options.outputFileName, options.verbosity)
+    else:
+        sys.exit("Cannot handle files with '%s' format." % (options.format))
+
+    writerNoAdaptor = None
+    if options.noAdaptor != None:
+        if options.format == "fasta":
+            writerNoAdaptor = FastaWriter(options.noAdaptor, options.verbosity)
+        elif options.format == "fastq":
+            writerNoAdaptor = FastqWriter(options.noAdaptor, options.verbosity)
+        else:
+            sys.exit("Cannot handle files with '%s' format." % (options.format))
+
+    nbFound = 0
+        
+    progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
+    for sequence in parser.getIterator():
+        progress.inc()
+        nucleotides = sequence.getSequence()
+        found       = False
+        for i in range(len(nucleotides) - minSize):
+            nucleotidesPart = nucleotides[i:]
+            adaptorPart     = options.adaptor if len(nucleotidesPart) >= len(options.adaptor) else options.adaptor[:len(nucleotidesPart)]
+            nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
+            if Utils.getHammingDistance(adaptorPart, nucleotidesPart) <= int(options.errors / 100.0 * len(adaptorPart)):
+                nbFound += 1
+                sequence.shrinkToFirstNucleotides(i)
+                writer.addSequence(sequence)
+                found = True
+                break
+        if not found:
+            writer.addSequence(sequence)
+            if writerNoAdaptor != None:
+                writerNoAdaptor.addSequence(sequence)
+    progress.done()
+
+    print "%d sequences with adaptors on %d (%.2f%%)" % (nbFound, parser.getNbSequences(), float(nbFound) / parser.getNbSequences() * 100)
+