--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/qualToFastq.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,87 @@
+#! /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.
+#
+import sys
+from optparse import OptionParser
+from commons.core.parsing.SequenceListParser import SequenceListParser
+from SMART.Java.Python.misc.Progress import Progress
+
+"""
+Transform qual and fasta files to a single fastq file
+"""
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Qual To FastQ v1.0.2: Convert a file in FASTA/Qual format to FastQ format. [Category: Conversion]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-f", "--fasta",     dest="fastaFileName",  action="store",               type="string", help="input fasta file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-q", "--qual",      dest="qualFileName",   action="store",               type="string", help="input qual file [compulsory] [format: file in TXT format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store", default=None, type="string", help="output file [compulsory] [format: output file in FASTQ format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+    
+    fastaFile = open(options.fastaFileName)
+    qualFile  = open(options.qualFileName)
+    fastqFile = open(options.outputFileName, "w")
+    
+    fastaLine = fastaFile.readline().strip()
+    qualLine  = qualFile.readline().strip()
+    header    = None
+    cpt       = 0
+    while fastaLine:
+        if not qualLine:
+            raise Exception("Qual file is shorter!")
+        if fastaLine[0] == ">":
+            header = fastaLine[1:]
+            if qualLine[0] != ">":
+                raise Exception("Discrepencies around %s!" % (header))
+            fastqFile.write("@%s\n" % (header))
+        else:
+            if qualLine[0] == ">":
+                raise Exception("Discrepencies around %s!" % (qualLine[1:]))
+            intQualities = qualLine.split()
+            if len(intQualities) != len(fastaLine):
+                raise Exception("Sizes of read and quality diverge in %s!" % (header))
+            chrQualities = [chr(min(int(quality), 93) + 33) for quality in intQualities]
+            fastqFile.write("%s\n+\n%s\n" % (fastaLine, "".join(chrQualities)))
+        fastaLine = fastaFile.readline().strip()
+        qualLine  = qualFile.readline().strip()
+        if cpt % 1000 == 0 and options.verbosity > 1:
+            sys.stdout.write("%d lines read\r" % (cpt))
+            sys.stdout.flush()
+        cpt += 1
+    if options.verbosity > 0:
+        print "%d lines read" % (cpt)
+        
+    if qualLine:
+        raise Exception("Qual file is longer!")
+