--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/fastqToFasta.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,96 @@
+#! /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.
+#
+"""Convert a FASTQ file to a FASTA file"""
+
+import os
+import sys
+from optparse import OptionParser
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+from math import *
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "FastQ to FastA v1.0.1: Convert a FastQ file into a FastA file. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in FASTQ format]")
+    parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [default: 1] [format: int]")
+    (options, args) = parser.parse_args()
+
+    inputFile = open(options.inputFileName)
+    outputFastaFile = open(options.outputFileName, "w")
+    
+    inSequenceName = False
+    inQualityName = False
+    inSequence = False
+    inQuality = True
+    sequenceName = None
+    lineNumber = 1
+    
+    for line in inputFile:
+
+        if inSequenceName:
+            inSequence = True
+            inSequenceName = False
+        elif inQualityName:
+            inQuality = True
+            inQualityName = False
+        elif inSequence:
+            inQualityName = True
+            inSequence = False
+        elif inQuality:
+            inSequenceName = True
+            inQuality = False
+        else:
+            sys.exit("Error! Do not in which section I am (line is %d)" % (lineNumber))
+
+        line = line.strip()
+        if inSequenceName:
+            if line[0] != "@":
+                sys.exit("Error! Sequence name '%s' does not start with '@' (line is %d)" % (line, lineNumber))
+            sequenceName = line[1:]
+            outputFastaFile.write(">%s\n" % (sequenceName))
+        elif inQualityName:
+            if line[0] != "+":
+                sys.exit("Error! Quality name '%s' does not start with '+' (line is %d)" % (line, lineNumber))
+            if len(line) > 1 and sequenceName != line[1:]:
+                sys.exit("Names in sequence and qual are different (%s, %s) (line is %d)" % (sequenceName, line[1:], lineNumber))
+        elif inSequence:
+            outputFastaFile.write("%s\n" % (line))
+        elif inQuality:
+            pass
+        lineNumber += 1
+    
+    inputFile.close()
+    outputFastaFile.close()