|
18
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3 ##@file
|
|
|
4 # Launch NWalign (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 'NWalign' (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 pyRepet.launcher.AbstractProgramLauncher import AbstractProgramLauncher
|
|
|
20 from commons.core.seq.AlignedBioseqDB import AlignedBioseqDB
|
|
|
21 from commons.core.coord.AlignUtils import AlignUtils
|
|
|
22
|
|
|
23
|
|
|
24 class NWalignProgramLauncher( AbstractProgramLauncher ):
|
|
|
25 """
|
|
|
26 Launch NWalign (pairwise alignment).
|
|
|
27 """
|
|
|
28
|
|
|
29 def __init__( self ):
|
|
|
30 """
|
|
|
31 Constructor.
|
|
|
32 """
|
|
|
33 AbstractProgramLauncher.__init__( self )
|
|
|
34 self._prgName = "NWalign"
|
|
|
35 self._formatInFile = "fasta"
|
|
|
36 self._sbjFile = ""
|
|
|
37 self._prgParam = ""
|
|
|
38 self._cmdLineSpecificOptions = "s:p:o:"
|
|
|
39
|
|
|
40
|
|
|
41 def getSpecificHelpAsString( self ):
|
|
|
42 """
|
|
|
43 Return the specific help as a string.
|
|
|
44 """
|
|
|
45 string = ""
|
|
|
46 string += "\nspecific options:"
|
|
|
47 string += "\n -s: name of the subject file (format='fasta')"
|
|
|
48 string += "\n -p: parameters for '%s'" % ( self.getProgramName() )
|
|
|
49 string += "\n -o: name of the output file (format='align', default=inFile+'.align')"
|
|
|
50 return string
|
|
|
51
|
|
|
52
|
|
|
53 def setASpecificAttributeFromCmdLine( self, o, a="" ):
|
|
|
54 """
|
|
|
55 Set a specific attribute from the command-line arguments.
|
|
|
56 """
|
|
|
57 if o =="-s":
|
|
|
58 self.setSubjectFile( a )
|
|
|
59 elif o == "-p":
|
|
|
60 self.setProgramParameters( a )
|
|
|
61 elif o == "-o":
|
|
|
62 self.setOutputFile( a )
|
|
|
63
|
|
|
64
|
|
|
65 def setSubjectFile( self, arg ):
|
|
|
66 self._sbjFile = arg
|
|
|
67
|
|
|
68
|
|
|
69 def getSubjectFile( self ):
|
|
|
70 return self._sbjFile
|
|
|
71
|
|
|
72
|
|
|
73 def checkSpecificAttributes( self ):
|
|
|
74 """
|
|
|
75 Check the specific attributes before running the program.
|
|
|
76 """
|
|
|
77 if self._sbjFile == "":
|
|
|
78 string = "ERROR: missing subject file (-s)"
|
|
|
79 print string
|
|
|
80 print self.getHelpAsString()
|
|
|
81 sys.exit(1)
|
|
|
82 if self.getOutputFile() == "":
|
|
|
83 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
|
|
|
84
|
|
|
85
|
|
|
86 def setWrapperCommandLine( self ):
|
|
|
87 """
|
|
|
88 Set the command-line of the wrapper.
|
|
|
89 Required for NWalignClusterLauncher.
|
|
|
90 """
|
|
|
91 self._wrpCmdLine = self.getWrapperName()
|
|
|
92 self._wrpCmdLine += " -i %s" % ( self.getInputFile() )
|
|
|
93 self._wrpCmdLine += " -s %s" % ( self.getSubjectFile() )
|
|
|
94 if self.getProgramParameters() != "":
|
|
|
95 self._wrpCmdLine += " -p '%s'" % ( self.getProgramParameters() )
|
|
|
96 if self.getOutputFile() == "":
|
|
|
97 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
|
|
|
98 self._wrpCmdLine += " -o %s" % ( self.getOutputFile() )
|
|
|
99 if self.getClean():
|
|
|
100 self._wrpCmdLine += " -c"
|
|
|
101 self._wrpCmdLine += " -v %i" % ( self.getVerbosityLevel() )
|
|
|
102
|
|
|
103
|
|
|
104 def setProgramCommandLine( self ):
|
|
|
105 """
|
|
|
106 Set the command-line of the program.
|
|
|
107 """
|
|
|
108 self._prgCmdLine = self.getProgramName()
|
|
|
109 if self.getProgramParameters() != "":
|
|
|
110 self._prgCmdLine += " %s" % ( self.getProgramParameters() )
|
|
|
111 self._prgCmdLine += " -o %s.afa" % ( self.getInputFile() )
|
|
|
112 self._prgCmdLine += " -v %i" % ( self.getVerbosityLevel() )
|
|
|
113 self._prgCmdLine += " %s" % ( self.getSubjectFile() )
|
|
|
114 self._prgCmdLine += " %s" % ( self.getInputFile() )
|
|
|
115
|
|
|
116
|
|
|
117 def setListFilesToKeep( self ):
|
|
|
118 """
|
|
|
119 Set the list of files to keep.
|
|
|
120 """
|
|
|
121 if self.getOutputFile() == "":
|
|
|
122 self.setOutputFile( "%s.afa" % ( self.getInputFile() ) )
|
|
|
123 self.appendFileToKeep( self.getOutputFile() )
|
|
|
124
|
|
|
125
|
|
|
126 def postprocess( self ):
|
|
|
127 absDB = AlignedBioseqDB( "%s.afa" % ( self.getInputFile() ) )
|
|
|
128 lHeaders = absDB.getHeaderList()
|
|
|
129 queryHeader = lHeaders[0]
|
|
|
130 subjectHeader = lHeaders[1]
|
|
|
131 queryLength = absDB.fetch( queryHeader ).getLength()
|
|
|
132 subjectLength = absDB.fetch( subjectHeader ).getLength()
|
|
|
133 lAligns = absDB.getAlignList( queryHeader, subjectHeader )
|
|
|
134 for i in lAligns:
|
|
|
135 if "re-oriented" in i.getQueryName():
|
|
|
136 i.setQueryName( queryHeader.replace(" re-oriented","") )
|
|
|
137 start = i.getQueryStart()
|
|
|
138 end = i.getQueryEnd()
|
|
|
139 i.setQueryStart( queryLength - end + 1 )
|
|
|
140 i.setQueryEnd( queryLength - start + 1 )
|
|
|
141 if "re-oriented" in i.getSubjectName():
|
|
|
142 i.setSubjectName( subjectHeader.replace(" re-oriented","") )
|
|
|
143 start = i.getSubjectStart()
|
|
|
144 end = i.getSubjectEnd()
|
|
|
145 i.setSubjectEnd( subjectLength - end + 1 )
|
|
|
146 i.setSubjectStart( subjectLength - start + 1 )
|
|
|
147 if not i.isQueryOnDirectStrand():
|
|
|
148 i.reverse()
|
|
|
149 AlignUtils.writeListInFile( lAligns, self.getOutputFile() )
|
|
|
150 os.remove( "%s.afa" % ( self.getInputFile() ) )
|
|
|
151
|
|
|
152
|
|
|
153 def setSummary( self ):
|
|
|
154 self._summary = "input file: %s" % ( self.getInputFile() )
|
|
|
155 self._summary += "\nsubject file: %s" % ( self.getSubjectFile() )
|
|
|
156 self._summary += "\nparameters: %s" % ( self.getProgramParameters() )
|
|
|
157 if self.getOutputFile() == "":
|
|
|
158 self.setOutputFile( "%s.align" % ( self.getInputFile() ) )
|
|
|
159 self._summary += "\noutput file: %s" % ( self.getOutputFile() )
|
|
|
160
|
|
|
161
|
|
|
162 def run( self ):
|
|
|
163 """
|
|
|
164 Run the program.
|
|
|
165 """
|
|
|
166 self.start()
|
|
|
167
|
|
|
168 self.setProgramCommandLine()
|
|
|
169 cmd = self.getProgramCommandLine()
|
|
|
170 if self.getVerbosityLevel() > 0:
|
|
|
171 print "LAUNCH: %s" % ( cmd )
|
|
|
172 sys.stdout.flush()
|
|
|
173 exitStatus = os.system( cmd )
|
|
|
174 if exitStatus != 0:
|
|
|
175 string = "ERROR: program '%s' returned exit status '%i'" % ( self.getProgramName(), exitStatus )
|
|
|
176 print string
|
|
|
177 sys.exit(1)
|
|
|
178
|
|
|
179 self.postprocess()
|
|
|
180
|
|
|
181 self.end()
|
|
|
182
|
|
|
183
|
|
|
184 if __name__ == "__main__":
|
|
|
185 i = NWalignProgramLauncher()
|
|
|
186 i.setAttributesFromCmdLine()
|
|
|
187 i.run()
|
