Mercurial > repos > dereeper > uniqprimer

comparison uniqprimer-0.5.0/primertools/programs.py @ 3:3249d78ecfc2 draft

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author dereeper
date Mon, 03 Jan 2022 09:56:55 +0000
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2:7e0438dad4e9 3:3249d78ecfc2
1 '''
2 Created on Jan 1, 2011
3
4 @author: John L. Herndon
5 @contact: herndon@cs.colostate.edu
6 @organization: Colorado State University
7 @group: Computer Science Department, Asa Ben-Hur's laboratory
8 '''
9
10
11 import utils
12 import os
13 import subprocess
14
15
16 class ProgramBase( object ):
17
18 def __init__( self ):
19
20 self.programName = None
21 self.proc = None
22
23 def getProcessArgs( self, args ):
24 crash #abstract
25
26 def execute( self, args, async = False ):
27 '''
28 run the nucmer program with a given compare file and an exclude file
29 '''
30
31 utils.logMessage( "ProgramBase::Execute( )", "Running the {0} program.".format( self.programName ) )
32
33 args, outputFile = self.getProcessArgs( args )
34
35 print "*** Running {0} ***".format( self.programName )
36
37 utils.logList( "ProgramBase::Execute( )", args )
38
39 proc = subprocess.Popen( args )
40
41 if async == False:
42 #wait for the nucmer instance to finish
43 proc.wait( )
44 print "*** Running {0} Complete ***".format( self.programName )
45
46 #return the name of the coords file
47 return outputFile
48
49 def isFinished( self ):
50 ifIsFinished
51
52 class Nucmer( ProgramBase ):
53
54 def __init__( self ):
55 #if we can't find the nucemer binary, throw
56 nucmerPath = utils.search_file( 'nucmer' )
57 ProgramBase.__init__( self )
58 if nucmerPath is None:
59 raise utils.ProgramNotFoundException( 'nucmer', "Please ensure that the MUMmer package is installed and configured on your system." )
60
61 self.nucmer = nucmerPath
62
63 self.programName = "nucmer"
64 self.outputExtension = ".coords"
65
66
67 def getProcessArgs( self, inputArgs ):
68
69
70 time = utils.getTimeStamp( )
71
72 identifier = "nucmer_alignments"
73 args = [ self.nucmer, '-p', identifier, '-o', '--minmatch', '300', '--maxgap', '1' ]
74
75 args.extend( inputArgs )
76
77 outputFile = "{0}.coords".format( identifier )
78
79 return args, outputFile
80
81 class Eprimer( ProgramBase ):
82
83 def __init__( self, eprimerOptions ):
84
85 self.programName = "EPrimer3"
86 self.options = eprimerOptions
87
88 primer3corePath = utils.search_file( "primer3_core" )
89 if primer3corePath is None:
90 raise utils.ProgramNotFoundException( "primer3_core", "Please ensure that the primer3 package is installed on your system. It can be obtained from http://primer3.sourceforge.net/" )
91
92 eprimerPath = utils.search_file( "eprimer3" )
93 if eprimerPath is None:
94 raise utils.ProgramNotFoundException( 'eprimer3', "Please ensure that the EMBOSS package is installed and configured on your system." )
95
96 self.primer3core = primer3corePath
97 self.eprimer3 = eprimerPath
98
99 def getProcessArgs( self, inputArgs ):
100
101 #todo - allow user to determine output file location/name
102
103 inputFasta = inputArgs[ 0 ]
104 outputFile = inputArgs[ 1 ]
105 args = [ self.eprimer3, inputFasta, outputFile, '-numreturn', '2', '-prange', self.options.getProductRange( ), '-osize', str( self.options.getPrimerSize( ) ),
106 '-minsize', str( self.options.getMinPrimerSize( ) ), '-maxsize', str( self.options.getMaxPrimerSize( ) )]
107
108 return args, outputFile
109
110 class PrimerSearch( ProgramBase ):
111 def __init__( self ):
112
113 self.programName = "PrimerSearch"
114 primerSearchPath = utils.search_file( "primersearch" )
115 if primerSearchPath is None:
116 raise utils.ProgramNotFoundException( "primersearch", "Please ensure that the EMBOSS package is installed on your system." )
117
118 self.primerSearch = primerSearchPath
119
120 def getProcessArgs( self, inputArgs ):
121 '''
122 usage for this program: inputArgs is an array length 4
123 inputArgs[0] = sequence file
124 inputArgs[1] = primer pairs file
125 inputArgs[2] = output file name
126 inputArgs[3] = percent mismatch
127 '''
128
129 args = [ self.primerSearch ]
130 args.extend( [ '-seqall', inputArgs[ 0 ] ] )
131 args.extend( [ '-infile', inputArgs[ 1 ] ] )
132 args.extend( [ '-mismatchpercent', inputArgs[ 3 ] ] )
133 args.extend( [ '-outfile', inputArgs[ 2 ] ] )
134
135
136 return args, inputArgs[ 2 ]
137
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141