--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/removeEmptySequences.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,135 @@
+#! /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.
+#
+"""
+Remove empty sequences from a FASTA or FASTQ file
+"""
+
+import os, random
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import *
+from commons.core.parsing.FastqParser import *
+from commons.core.writer.FastaWriter import *
+from commons.core.writer.FastqWriter import *
+from SMART.Java.Python.misc.Progress import *
+
+
+class EmptySequenceRemover(object):
+
+    def __init__(self, verbosity = 1):
+        self.verbosity            = verbosity
+        self.inputFileName    = None
+        self.parser                 = None
+        self.format                 = None
+        self.writer                 = None
+        self.forbiddenNames = {}
+        self.removedNames     = {}
+
+
+    def setInputFileName(self, fileName, format):
+        self.inputFileName = fileName
+        self.format                = format
+        if options.format == "fasta":
+            self.parser = FastaParser(self.inputFileName, self.verbosity)
+        elif options.format == "fastq":
+            self.parser = FastqParser(self.inputFileName, self.verbosity)
+        else:
+            sys.exit("Do not understand '%s' file format." % (self.format))
+
+
+    def setOutputFileName(self, fileName):
+        if options.format == "fasta":
+            self.writer = FastaWriter("%s.mfa" % (fileName), self.verbosity)
+        elif options.format == "fastq":
+            self.writer = FastqWriter("%s.mfq" % (fileName), self.verbosity)
+
+
+    def parse(self):
+        progress = Progress(self.parser.getNbSequences(), "Reading sequences in %s" % (options.inputFileName), options.verbosity)
+        for sequence in self.parser.getIterator():
+            name = sequence.name.split("/")[0]
+            if name not in self.forbiddenNames:
+                if sequence.sequence == "":
+                    self.removedNames[name] = 1
+                else:
+                    self.writer.addSequence(sequence)
+            progress.inc()
+        progress.done()
+        self.writer.write()
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Remove Empty Sequences v1.0.2: Remove all the empty sequences in a list. [Category: Personal]"
+
+    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 the input file [compulsory] [format: sequence file format]")
+    parser.add_option("-j", "--input2",        dest="inputFileName2",    action="store",                                         type="string", help="input file 2 (in case of pair end reads) [format: file in sequence format given by -f] [default: None]")
+    parser.add_option("-o", "--output",        dest="outputFileName",    action="store",            default=None,    type="string", help="output file [compulsory] [format: output file in format given by -f]")
+    parser.add_option("-p", "--output2",     dest="outputFileName2", action="store",            default=None,    type="string", help="output file 2 (in case of pair end reads) [format: output file in sequence format given by -f] [default: None]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",             action="store",            default=1,         type="int",        help="trace level [format: int] [default: 1]")
+    parser.add_option("-l", "--log",             dest="log",                         action="store_true", default=False,                                help="write a log file [format: bool] [default: false]")
+    (options, args) = parser.parse_args()
+
+    if options.log:
+        logHandle = open("%s.log" % options.outputFileName, "w")
+    
+    remover = EmptySequenceRemover(options.verbosity)
+    remover.setInputFileName(options.inputFileName, options.format)
+    remover.setOutputFileName(options.outputFileName)
+    remover.parse()
+    removedNames = remover.removedNames
+    if options.log:
+        for name in removedNames:
+            logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName))
+    nbSequences = remover.parser.getNbSequences()
+
+    newRemovedNames = {}
+    if options.inputFileName2 != None:
+        remover = EmptySequenceRemover(options.verbosity)
+        remover.setInputFileName(options.inputFileName2, options.format)
+        remover.setOutputFileName(options.outputFileName2)
+        remover.forbiddenNames = removedNames
+        remover.parse()
+        newRemovedNames = remover.removedNames
+        if options.log:
+            for name in newRemovedNames:
+                logHandle.write("Removed '%s' in %s\n" % (name, options.inputFileName2))
+
+        remover = EmptySequenceRemover(options.verbosity)
+        remover.setInputFileName(options.inputFileName, options.format)
+        remover.setOutputFileName(options.outputFileName)
+        remover.forbiddenNames = newRemovedNames
+        remover.parse()
+
+    nbRemoved = len(removedNames.keys()) + len(newRemovedNames.keys())
+    print "%d over %d sequences are empty (%.2f%%)." % (nbRemoved, nbSequences, float(nbRemoved) / nbSequences * 100)