diff smart_toolShed/SMART/Java/Python/wrongFastqToQual.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/wrongFastqToQual.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,81 @@
+#! /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 pseudo-FASTQ file to QUAL files"""
+
+import os
+from optparse import OptionParser
+from SMART.Java.Python.misc.Progress import *
+from math import *
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Wrong FastQ to Qual v1.0.1: Convert a pseudo-FastQ (i.e. a FastQ file with a wrong format) into a Qual 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 QUAL format]")
+    parser.add_option("-v", "--verbosity",    dest="verbosity",                 action="store",            default=1,                type="int",        help="trace level [format: int] [default: 1]")
+    (options, args) = parser.parse_args()
+
+    inputFile             = open(options.inputFileName)
+    outputFastaFile = open("%s.fasta" % (options.outputFileName), "w")
+    outputQualFile    = open("%s.qual" % (options.outputFileName), "w")
+    
+    inSequence     = False
+    inQuality        = True
+    sequenceName = None
+    for line in inputFile:
+        line = line.strip()
+        if line[0] == "@":
+            if inQuality == False:
+                sys.exit("Quality of %s is missing" % (sequenceName))
+            inSequence     = True
+            inQuality        = False
+            sequenceName = line[1:]
+            outputFastaFile.write(">%s\n" % (sequenceName))
+        elif line[0] == "+":
+            if inSequence == False:
+                sys.exit("Sequence of %s is missing" % (line[1:]))
+            inSequence     = False
+            inQuality        = True
+            if sequenceName != line[1:]:
+                sys.exit("Names in sequence and qual are different (%s, %s)" % (sequenceName, line[1:]))
+            outputQualFile.write(">%s\n" % (sequenceName))
+        else:
+            if inSequence:
+                outputFastaFile.write("%s\n" % (line))
+            elif inQuality:
+                outputQualFile.write("%s\n" % (line))
+    
+    inputFile.close()
+    outputFastaFile.close()
+    outputQualFile.close()