diff SMART/Java/Python/sequenceListSplitter.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/sequenceListSplitter.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,73 @@
+#! /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.
+#
+"""Split a FASTA file into several shorter ones"""
+
+from optparse import OptionParser
+from commons.core.parsing.SequenceListParser import *
+from commons.core.writer.FastaWriter import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Sequence List Splitter v1.0.1: Split a list of big sequences into small chunks. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",   action="store",                         type="string", help="input file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-o", "--output",    dest="outputFileNames", action="store",                         type="string", help="output files [compulsory] [format: output file in FASTA format]")
+    parser.add_option("-n", "--number",    dest="number",          action="store",      default=10,        type="int",    help="number of splits [compulsory] [format: int] [default: 10]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",       action="store",      default=1,         type="int",    help="trace level [format: int]")
+    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(options.outputFileNames + ".log", "w")
+
+    # split file
+    sequenceListParser = SequenceListParser(options.inputFileName, options.verbosity)
+    nbSequences                = sequenceListParser.getNbSequences()
+    nbSequencesByFile    = math.ceil(nbSequences / options.number)
+
+    # write into files
+    currentFileNumber = 1
+    writer            = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
+    nbSequencesHere   = 0
+    progress          = Progress(nbSequences, "Writing files", options.verbosity)
+    for sequence in sequenceListParser.getIterator():
+        writer.addSequence(sequence)
+        nbSequencesHere += 1
+        if nbSequencesHere == nbSequencesByFile:
+            currentFileNumber += 1
+            writer             = FastaWriter("%s%i.fasta" % (options.outputFileNames, currentFileNumber), options.verbosity)
+            nbSequencesHere    = 0
+        progress.inc()
+    progress.done()