Mercurial > repos > yufei-luo > s_mart

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

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author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
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30:5677346472b5 31:0ab839023fe4
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()