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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/modifySequenceList.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,72 @@
+#! /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.
+#
+"""Modify the content of a FASTA file"""
+import sys
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import FastaParser
+from commons.core.parsing.FastqParser import FastqParser
+from commons.core.writer.FastaWriter import FastaWriter
+from commons.core.writer.FastqWriter import FastqWriter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Modify Sequence List v1.0.1: Extend or shring a list of sequences. [Category: Data Modification]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input", dest="inputFileName",action="store", type="string", help="input file [compulsory] [format: file in format given by -f]")
+    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("-f", "--format", dest="format",action="store",type="string", help="format of the file [compulsory] [format: sequence file format]")
+    parser.add_option("-s", "--start", dest="start", action="store", default=None,type="int",help="keep first nucleotides [format: int]")
+    parser.add_option("-e", "--end",  dest="end", action="store",default=None,type="int",help="keep last nucleotides [format: int]")
+    parser.add_option("-v", "--verbosity",dest="verbosity",action="store",default=1,type="int",help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    if options.format == "fasta":
+        parser = FastaParser(options.inputFileName, options.verbosity)
+        writer = FastaWriter(options.outputFileName, options.verbosity)
+    elif options.format == "fastq":
+        parser = FastqParser(options.inputFileName, options.verbosity)
+        writer = FastqWriter(options.outputFileName, options.verbosity)
+    else:
+        sys.exit("Do not understand '%s' file format." % (options.format))
+
+    progress = Progress(parser.getNbSequences(), "Reading file %s" % (options.inputFileName), options.verbosity)
+    for sequence in parser.getIterator():
+        if options.start != None:
+            sequence.shrinkToFirstNucleotides(options.start)
+        if options.end != None:
+            sequence.shrinkToLastNucleotides(options.end)
+        writer.addSequence(sequence)
+        progress.inc()
+    progress.done()