Mercurial > repos > yufei-luo > s_mart
comparison commons/tools/dbConsensus.py @ 18:94ab73e8a190
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author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:20:15 -0400 |
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17:b0e8584489e6 | 18:94ab73e8a190 |
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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 import os | |
34 import sys | |
35 import getopt | |
36 | |
37 ##@file | |
38 # usage: dbConsensus.py [ options ] | |
39 # options: | |
40 # -h: this help | |
41 # -i: name of the input file (format=aligned fasta) | |
42 # -n: minimum number of nucleotides in a column to edit a consensus (default=1) | |
43 # -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0) | |
44 # -o: name of the output file (default=inFileName+'.cons') | |
45 # -v: verbose (default=0/1/2) | |
46 | |
47 if not os.environ.has_key( "REPET_PATH" ): | |
48 print "ERROR: no environment variable REPET_PATH" | |
49 sys.exit(1) | |
50 sys.path.append( os.environ["REPET_PATH"] ) | |
51 | |
52 import commons.core.seq.AlignedBioseqDB | |
53 | |
54 | |
55 def help(): | |
56 """ | |
57 Give the list of the command-line options. | |
58 """ | |
59 print | |
60 print "usage:",sys.argv[0]," [ options ]" | |
61 print "options:" | |
62 print " -h: this help" | |
63 print " -i: name of the input file (format=aligned fasta)" | |
64 print " -n: minimum number of nucleotides in a column to edit a consensus (default=1)" | |
65 print " -p: minimum proportion for the major nucleotide to be used, otherwise add 'N' (default=0.0)" | |
66 print " -o: name of the output file (default=inFileName+'.cons')" | |
67 print " -H: format the header with pyramid and piles informations (SATannot)" | |
68 print " -v: verbose (default=0/1/2)" | |
69 print | |
70 | |
71 | |
72 def main(): | |
73 | |
74 inFileName = "" | |
75 minNbNt = 1 | |
76 minPropNt = 0.0 | |
77 outFileName = "" | |
78 header_SATannot = False | |
79 verbose = 0 | |
80 | |
81 try: | |
82 opts, args = getopt.getopt(sys.argv[1:],"hi:n:p:o:v:H") | |
83 except getopt.GetoptError, err: | |
84 print str(err); help(); sys.exit(1) | |
85 for o,a in opts: | |
86 if o == "-h": | |
87 help() | |
88 sys.exit(0) | |
89 elif o == "-i": | |
90 inFileName = a | |
91 elif o == "-n": | |
92 minNbNt = int(a) | |
93 elif o == "-p": | |
94 minPropNt = float(a) | |
95 elif o == "-o": | |
96 outFileName = a | |
97 elif o == "-H": | |
98 header_SATannot = True | |
99 elif o == "-v": | |
100 verbose = int(a) | |
101 | |
102 if inFileName == "": | |
103 print "ERROR: missing input file name" | |
104 help() | |
105 sys.exit(1) | |
106 | |
107 if verbose > 0: | |
108 print "START %s" % (sys.argv[0].split("/")[-1]) | |
109 sys.stdout.flush() | |
110 | |
111 alnDB = commons.core.seq.AlignedBioseqDB.AlignedBioseqDB( inFileName ) | |
112 | |
113 if alnDB.getSize() < minNbNt: | |
114 print "WARNING: not enough sequences (<%i)" % ( minNbNt ) | |
115 | |
116 else: | |
117 consensus = alnDB.getConsensus( minNbNt, minPropNt, verbose, header_SATannot) | |
118 if consensus != None: | |
119 consensus.upCase() | |
120 if outFileName == "": | |
121 outFileName = "%s.cons" % ( inFileName ) | |
122 outFile = open( outFileName, "w" ) | |
123 consensus.write( outFile ) | |
124 outFile.close() | |
125 | |
126 if verbose > 0: | |
127 print "END %s" % (sys.argv[0].split("/")[-1]) | |
128 sys.stdout.flush() | |
129 | |
130 return 0 | |
131 | |
132 if __name__ == "__main__": | |
133 main () |