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comparison commons/launcher/LaunchLastZ.py @ 31:0ab839023fe4

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
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30:5677346472b5 31:0ab839023fe4
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 sys
34 import os
35 import optparse
36 from commons.core.checker.CheckerUtils import CheckerUtils
37 from commons.core.utils.FileUtils import FileUtils
38 from subprocess import Popen
39 from commons.core.utils.RepetOptionParser import RepetOptionParser
40 import subprocess
41 import tempfile
42
43 class LaunchLastZ(object):
44
45 def __init__(self,queryFileName="", refFileName ="", outputFileName=None,outputFileFormat="axt",noTransition=True, ambiguous=None, step=1,gfextend=False, chain=False, verbosity=1 ):
46 self.queryFileName = queryFileName
47 self.refFileName = refFileName
48 self.outputFileName = outputFileName
49 self.outputFileFormat = outputFileFormat
50 self.noTransition = noTransition
51 self.step = step
52 self.ambiguous = ambiguous
53 self.gfextend = gfextend
54 self.chain = chain
55 self.verbosity = verbosity
56
57 def setAttributesFromCmdLine(self):
58 description = "LaunchLastZ runs the LastZ program ."
59 parser = RepetOptionParser(description = description)
60 parser.add_option("-q", "--query", dest="queryFileName", default = None, action="store", type="string", help="input query file [compulsory] [format: fasta]")
61 parser.add_option("-r", "--ref", dest="refFileName", default = None, action="store", type="string", help="input ref file [compulsory] [format: fasta]")
62 parser.add_option("-o", "--output", dest="outputFileName", default = None, action="store", type="string", help="output file [compulsory] ")
63 parser.add_option("-f", "--format", dest="outputFileFormat", default = "axt", action="store", type="string", help="output file format[optional] ")
64 parser.add_option("-n", "--notransition", dest="noTransition", action="store_false", default=True, help="noTransition (default True) [optional] ")
65 parser.add_option("-a", "--ambiguous", dest="ambiguous", action="store", type="string", help="ambiguous [optional] ")
66 parser.add_option("-s", "--step", dest="step", default = 1, action="store", type="int", help="stepsize (default 1) [optional] ")
67 parser.add_option("-g", "--gfextend", dest="gfextend", action="store_true", help="extend gf (default false)[optional] ")
68 parser.add_option("-c", "--chain", dest="chain", action="store_true", help="chain (default false)[optional] ")
69 parser.add_option("-v", "--verbosity", dest="verbosity", default = 1, action="store", type="int", help="verbosity [optional] ")
70 (self._options, args) = parser.parse_args()
71 self._setAttributesFromOptions(self._options)
72
73 def _setAttributesFromOptions(self, options):
74 self.queryFileName = options.queryFileName
75 self.refFileName = options.refFileName
76 self.outputFileName = options.outputFileName
77 self.outputFileFormat = options.outputFileFormat
78 self.ambiguous = options.ambiguous
79 self.noTransition = options.noTransition
80 self.step = options.step
81 self.gfextend = options.gfextend
82 self.chain = options.chain
83 self.verbosity = options.verbosity
84
85 def checkOptions(self):
86 if self.queryFileName != "":
87 if not FileUtils.isRessourceExists(self.queryFileName):
88 raise Exception("ERROR: Query file does not exist!")
89 else:
90 raise Exception("ERROR: No specified --query option!")
91 if self.refFileName != "":
92 if not FileUtils.isRessourceExists(self.refFileName):
93 raise Exception("ERROR: Ref file does not exist!")
94 else:
95 raise Exception("ERROR: No specified --ref option!")
96 if self.outputFileName == None:
97 self.outputFileName = "%s_%s.axt" % (os.path.basename(self.queryFileName), os.path.basename(self.refFileName))
98
99 def run(self):
100 if not CheckerUtils.isExecutableInUserPath("lastz") :
101 print ("ERROR: LastZ must be in your path")
102 else:
103 self.checkOptions()
104
105 transition = ""
106 if self.noTransition:
107 transition = "--notransition"
108 ambiguous = ""
109 if self.ambiguous is not None:
110 ambiguous = "--ambiguous=%s" % self.ambiguous
111
112 gfextend = ""
113 if self.gfextend:
114 gfextend = "--gfextend"
115
116 chain = ""
117 if self.chain:
118 chain = "--chain"
119
120 cmd = "lastz %s[format=fasta] %s[format=fasta] --output=%s --format=%s %s %s --step=%i %s %s" % (self.refFileName, self.queryFileName, self.outputFileName
121 , self.outputFileFormat, ambiguous, transition,self.step, gfextend, chain)
122 if self.verbosity>0:
123 print("Running LastZ with following commands : %s" %cmd)
124 sys.stdout.flush()
125 cmd = cmd.split()
126 process = subprocess.Popen(cmd)
127 process.wait()
128 return process.returncode
129
130 if __name__ == "__main__":
131 iLaunchLastZ = LaunchLastZ()
132 iLaunchLastZ.setAttributesFromCmdLine()
133 iLaunchLastZ.run()