--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/trimSequences.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,149 @@
+#! /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.
+#
+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 Sequences v1.0.3: Remove the 5' and/or 3' adaptors 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("-3", "--threePAdaptor", dest="threePAdaptor",  action="store",      default=None,  type="string", help="3' adaptor [format: string] [default: None]")
+    parser.add_option("-5", "--fivePAdaptor",  dest="fivePAdaptor",   action="store",      default=None,  type="string", help="5' adaptor [format: string] [default: None]")
+    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("-d", "--indels",        dest="indels",         action="store_true", default=False,                help="also accept indels [format: bool] [default: False]")
+    parser.add_option("-n", "--noAdaptor5p",   dest="noAdaptor5p",    action="store",      default=None,  type="string", help="print sequences with no 5' adaptor [format: output file in sequence format given by -f]")
+    parser.add_option("-m", "--noAdaptor3p",   dest="noAdaptor3p",    action="store",      default=None,  type="string", help="print sequences with no 3' 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 = 3
+
+    if options.format == "fasta":
+        parser = FastaParser(options.inputFileName, options.verbosity)
+    elif options.format == "fastq":
+        parser = FastqParser(options.inputFileName, options.verbosity)
+    else:
+        raise Exception("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:
+        raise Exception("Cannot handle files with '%s' format." % (options.format))
+
+
+    if options.noAdaptor5p != None:
+        if options.format == "fasta":
+            writer5pNoAdaptor = FastaWriter(options.noAdaptor5p, options.verbosity)
+        elif options.format == "fastq":
+            writer5pNoAdaptor = FastqWriter(options.noAdaptor5p, options.verbosity)
+        else:
+            raise Exception("Cannot handle files with '%s' format." % (options.format))
+    nbFound5p = 0
+    
+    if options.noAdaptor3p != None:
+        if options.format == "fasta":
+            writer3pNoAdaptor = FastaWriter(options.noAdaptor3p, options.verbosity)
+        elif options.format == "fastq":
+            writer3pNoAdaptor = FastqWriter(options.noAdaptor3p, options.verbosity)
+        else:
+            raise Exception("Cannot handle files with '%s' format." % (options.format))
+    nbFound3p = 0
+            
+    progress = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
+    for sequence in parser.getIterator():
+        progress.inc()
+        if options.threePAdaptor != None:
+            nucleotides = sequence.sequence
+            found       = False
+            bestScore   = 10000
+            bestRegion  = 0
+            for i in range(len(nucleotides) - minSize):
+                nucleotidesPart = nucleotides[i:]
+                adaptorPart     = options.threePAdaptor if len(nucleotidesPart) >= len(options.threePAdaptor) else options.threePAdaptor[:len(nucleotidesPart)]
+                nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[:len(adaptorPart)]
+                if options.indels:
+                    score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
+                else:
+                    score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
+                if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
+                    bestScore  = score
+                    bestRegion = i
+                    found      = True
+            if found:
+                nbFound3p += 1
+                sequence.shrinkToFirstNucleotides(bestRegion)
+            elif options.noAdaptor3p:
+                writer3pNoAdaptor.addSequence(sequence)
+        if options.fivePAdaptor != None:
+            nucleotides = sequence.sequence
+            found       = False
+            bestScore   = 10000
+            bestRegion  = 0
+            for i in reversed(range(minSize, len(nucleotides))):
+                nucleotidesPart = nucleotides[:i]
+                adaptorPart     = options.fivePAdaptor if len(nucleotidesPart) >= len(options.fivePAdaptor) else options.fivePAdaptor[-len(nucleotidesPart):]
+                nucleotidesPart = nucleotidesPart if len(adaptorPart) == len(nucleotidesPart) else nucleotidesPart[-len(adaptorPart):]
+                if options.indels:
+                    score = Utils.getLevenshteinDistance(adaptorPart, nucleotidesPart)
+                else:
+                    score = Utils.getHammingDistance(adaptorPart, nucleotidesPart)
+                if score <= int(options.errors / 100.0 * len(adaptorPart)) and score < bestScore:
+                    bestScore  = score
+                    bestRegion = i
+                    found      = True
+            if found:
+                nbFound5p += 1
+                sequence.shrinkToLastNucleotides(len(nucleotides) - bestRegion)
+            elif options.noAdaptor5p:
+                writer5pNoAdaptor.addSequence(sequence)
+        writer.addSequence(sequence)
+    progress.done()
+    writer.close()
+
+    print "%d sequences" % (parser.getNbSequences())
+    if options.fivePAdaptor != None:
+        print "%d sequences with 5' adaptors (%.2f%%)" % (nbFound5p, float(nbFound5p) / parser.getNbSequences() * 100)
+    if options.threePAdaptor != None:
+        print "%d sequences with 3' adaptors (%.2f%%)" % (nbFound3p, float(nbFound3p) / parser.getNbSequences() * 100)
+