Mercurial > repos > yufei-luo > s_mart

comparison commons/launcher/BlatProgramLauncher.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 ##@file
4 # Launch Blat (pairwise alignment).
5 #
6 # options:
7 # -h: this help
8 # -i: name of the input file (queries, format='fasta')
9 # -s: name of the subject file (format='fasta')
10 # -p: parameters for 'blat' (default='-d 2')
11 # -o: name of the output file (format='align', default=inFile+'.align')
12 # -c: clean
13 # -v: verbosity level (default=0/1)
14
15
16 import os
17 import sys
18
19 from commons.pyRepetUnit.components.AbstractProgramLauncher import AbstractProgramLauncher
20
21
22 class BlatProgramLauncher( AbstractProgramLauncher ):
23 """
24 Launch Blat (pairwise alignment).
25 """
26
27 def __init__( self ):
28 """
29 Constructor.
30 """
31 AbstractProgramLauncher.__init__( self )
32 self._prgName = "blat"
33 self._formatInFile = "fasta"
34 self._sbjFile = ""
35 self._prgParam = ""
36 self._allByAll = False
37
38
39 def getHelpAsString( self ):
40 string = AbstractProgramLauncher.getHelpAsString(self)
41 string += "\nspecific options:"
42 string += "\n -s: name of the subject file (database, format='fasta')"
43 string += "\n -p: parameters for '%s'" % ( self.getProgramName() )
44 string += "\n -A: same sequences (all-by-all)"
45 string += "\n -o: name of the output file (format='align', default=inFile+'.align')"
46 return string
47
48 def getCmdLineOptions(self):
49 return AbstractProgramLauncher.getCmdLineOptions(self) + "s:p:Ao:"
50
51 def setAttributesFromCmdLine( self, o, a = "" ):
52 AbstractProgramLauncher.setAttributesFromCmdLine(self, o, a)
53 if o == "-s":
54 self.setSubjectFile( a )
55 elif o == "-p":
56 self.setProgramParameters( a )
57 elif o == "-A":
58 self.setAllByAll()
59 elif o == "-o":
60 self.setOutputFile( a )
61
62
63 def setSubjectFile( self, arg ):
64 self._sbjFile = arg
65
66
67 def getSubjectFile( self ):
68 return self._sbjFile
69
70
71 def setAllByAll( self ):
72 self._allByAll = True
73
74
75 def getAllByAll( self ):
76 return self._allByAll
77
78
79 def check( self ):
80 """
81 Check the specific attributes before running the program.
82 """
83 AbstractProgramLauncher.check(self)
84 if self._sbjFile == "":
85 string = "ERROR: missing subject file (-s)"
86 print string
87 print self.getHelpAsString()
88 sys.exit(1)
89 if self.getOutputFile() == "":
90 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
91
92
93 def setWrapperCommandLine( self ):
94 """
95 Set the command-line of the wrapper.
96 Required for BlatClusterLauncher.
97 """
98 self._wrpCmdLine = self.getWrapperName()
99 self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
100 self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
101 if self.getProgramParameters() != "":
102 self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
103 if self.getAllByAll():
104 self._wrpCmdLine += " -A"
105 if self.getOutputFile() == "":
106 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
107 self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
108 if self.getClean():
109 self._wrpCmdLine += " -c"
110 self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
111
112
113 def setProgramCommandLine( self ):
114 """
115 Set the command-line of the program.
116 """
117 self._prgCmdLine = self.getProgramName()
118 self._prgCmdLine += " %s" % ( self.getSubjectFile() )
119 self._prgCmdLine += " %s" % ( self.getInputFile() )
120 if self.getProgramParameters() != "":
121 self._prgCmdLine += " %s" % ( self.getProgramParameters() )
122 self._prgCmdLine += " -out=blast8"
123 self._prgCmdLine += " %s.blast" % ( self.getInputFile() )
124
125
126 def setListFilesToKeep( self ):
127 """
128 Set the list of files to keep.
129 """
130 if self.getOutputFile() == "":
131 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
132 self.appendFileToKeep( self.getOutputFile() )
133
134
135 def setListFilesToRemove( self ):
136 """
137 Set the list of files to remove.
138 """
139 self.appendFileToRemove( "%s.blast" % ( self.getInputFile() ) )
140
141
142 def convertBlastIntoAlign( self ):
143 """
144 Convert a 'blast' file into the 'align' format.
145 """
146 cmd = os.environ["REPET_PATH"] + "/bin/blast2align.py"
147 cmd += " -i %s.blast" % ( self.getInputFile() )
148 cmd += " -o %s" % ( self.getOutputFile() )
149 exitStatus = os.system( cmd )
150 if exitStatus != 0:
151 string = "ERROR while converting 'blast' file into 'align' format"
152 print string
153 sys.exit(1)
154
155
156 def setSummary( self ):
157 self._summary = "input file: %s" % ( self.getInputFile() )
158 self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
159 self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
160 if self.getAllByAll():
161 self._summary += "\nall-by-all"
162 if self.getOutputFile() == "":
163 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
164 self._summary += "\noutput file: %s" % ( self.getOutputFile() )
165
166
167 def run( self ):
168 """
169 Run the program.
170 """
171 self.start()
172
173 self.setProgramCommandLine()
174 cmd = self.getProgramCommandLine()
175 if self.getVerbosityLevel() > 0:
176 print "LAUNCH: %s" % ( cmd )
177 sys.stdout.flush()
178 exitStatus = os.system( cmd )
179 if exitStatus != 0:
180 string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
181 print string
182 sys.exit(1)
183
184 self.convertBlastIntoAlign()
185
186 self.end()
187
188
189 if __name__ == "__main__":
190 i = BlatProgramLauncher()
191 i.checkAttributesFromCmdLine()
192 i.run()