Mercurial > repos > yufei-luo > s_mart

comparison commons/tools/dbShuffle.py @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 #!/usr/bin/env python
2
3 # Copyright INRA (Institut National de la Recherche Agronomique)
4 # http://www.inra.fr
5 # http://urgi.versailles.inra.fr
6 #
7 # This software is governed by the CeCILL license under French law and
8 # abiding by the rules of distribution of free software. You can use,
9 # modify and/ or redistribute the software under the terms of the CeCILL
10 # license as circulated by CEA, CNRS and INRIA at the following URL
11 # "http://www.cecill.info".
12 #
13 # As a counterpart to the access to the source code and rights to copy,
14 # modify and redistribute granted by the license, users are provided only
15 # with a limited warranty and the software's author, the holder of the
16 # economic rights, and the successive licensors have only limited
17 # liability.
18 #
19 # In this respect, the user's attention is drawn to the risks associated
20 # with loading, using, modifying and/or developing or reproducing the
21 # software by the user in light of its specific status of free software,
22 # that may mean that it is complicated to manipulate, and that also
23 # therefore means that it is reserved for developers and experienced
24 # professionals having in-depth computer knowledge. Users are therefore
25 # encouraged to load and test the software's suitability as regards their
26 # requirements in conditions enabling the security of their systems and/or
27 # data to be ensured and, more generally, to use and operate it in the
28 # same conditions as regards security.
29 #
30 # The fact that you are presently reading this means that you have had
31 # knowledge of the CeCILL license and that you accept its terms.
32
33
34 import os
35 import sys
36 import getopt
37
38 from commons.core.seq.FastaUtils import FastaUtils
39
40
41 def help():
42 print
43 print "usage: %s [ options ]" % ( sys.argv[0].split("/")[-1] )
44 print "options:"
45 print " -h: this help"
46 print " INPUT: use '-i' or '-I'"
47 print " -i: name of the input file (fasta format)"
48 print " -I: name of the input directory (containing fasta files)"
49 print " OUTPUT: use '-o' or '-O'"
50 print " -o: name of the output file (use only with '-i')"
51 print " -O: name of the output directory (use only with '-I')"
52 print " output file are: prefix of input fasta file + '_shuffle.fa')"
53 print " -v: verbose (default=0/1/2)"
54 print
55
56
57 def main():
58 inData = ""
59 outData = ""
60 verbose = 0
61 try:
62 opts, args = getopt.getopt( sys.argv[1:], "hi:I:o:O:v:" )
63 except getopt.GetoptError, err:
64 sys.stderr.write( "%s\n" % str(err) )
65 help()
66 sys.exit(1)
67 for o,a in opts:
68 if o == "-h":
69 help()
70 sys.exit(0)
71 elif o == "-i":
72 inData = a
73 elif o == "-I":
74 inData = a
75 elif o == "-o":
76 outData = a
77 elif o == "-O":
78 outData = a
79 elif o == "-v":
80 verbose = int(a)
81
82 if inData == "" or ( not os.path.isfile( inData ) \
83 and not os.path.isdir( inData ) ):
84 msg = "ERROR: missing input file or directory (-i or -I)"
85 sys.stderr.write( "%s\n" % msg )
86 help()
87 sys.exit(1)
88
89 if outData == "":
90 print "ERROR: missing name of output file or directory (-o or -O)"
91 help()
92 sys.exit(1)
93
94 if verbose > 0:
95 print "START %s" % ( sys.argv[0].split("/")[-1] )
96 sys.stdout.flush()
97
98 FastaUtils.dbShuffle( inData, outData, verbose )
99
100 if verbose > 0:
101 print "END %s" % ( sys.argv[0].split("/")[-1] )
102 sys.stdout.flush()
103
104 return 0
105
106
107 if __name__ == "__main__":
108 main()