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comparison SMART/Java/Python/txtToFasta.py @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
parents 769e306b7933
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37:d22fadc825e3 38:2c0c0a89fad7
1 #! /usr/bin/env python
2 #
3 # Copyright INRA-URGI 2009-2010
4 #
5 # This software is governed by the CeCILL license under French law and
6 # abiding by the rules of distribution of free software. You can use,
7 # modify and/ or redistribute the software under the terms of the CeCILL
8 # license as circulated by CEA, CNRS and INRIA at the following URL
9 # "http://www.cecill.info".
10 #
11 # As a counterpart to the access to the source code and rights to copy,
12 # modify and redistribute granted by the license, users are provided only
13 # with a limited warranty and the software's author, the holder of the
14 # economic rights, and the successive licensors have only limited
15 # liability.
16 #
17 # In this respect, the user's attention is drawn to the risks associated
18 # with loading, using, modifying and/or developing or reproducing the
19 # software by the user in light of its specific status of free software,
20 # that may mean that it is complicated to manipulate, and that also
21 # therefore means that it is reserved for developers and experienced
22 # professionals having in-depth computer knowledge. Users are therefore
23 # encouraged to load and test the software's suitability as regards their
24 # requirements in conditions enabling the security of their systems and/or
25 # data to be ensured and, more generally, to use and operate it in the
26 # same conditions as regards security.
27 #
28 # The fact that you are presently reading this means that you have had
29 # knowledge of the CeCILL license and that you accept its terms.
30 #
31 """Transform a plain text file to a FASTA file"""
32
33 import os
34 from optparse import OptionParser
35 from SMART.Java.Python.structure.Sequence import *
36 from SMART.Java.Python.misc.Progress import *
37
38
39 if __name__ == "__main__":
40
41 # parse command line
42 parser = OptionParser()
43 description = "Txt to Fasta v1.0.1: Convert a Txt file (one sequence per line) into Fasta file. [Category: Personnal]"
44
45 parser = OptionParser(description = description)
46 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in TXT format]")
47 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in FASTA format]")
48 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
49 (options, args) = parser.parse_args()
50
51 inputFile = open(options.inputFileName)
52 outputFile = open(options.outputFileName, "w")
53
54 for line in inputFile:
55 line = line.strip()
56 splittedLine = line.split()
57 sequence = splittedLine[0]
58 nb = 1 if len(splittedLine) == 1 else int(splittedLine[1])
59 for i in range(nb):
60 outputFile.write(">%s\n%s\n" % (sequence, sequence))
61
62 inputFile.close()
63 outputFile.close()