Mercurial > repos > dereeper > uniqprimer

comparison uniqprimer-0.5.0/utils.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 exceptions
12 import time
13 import os.path
14 from os import pathsep
15 from string import split
16 import tempfile
17 import shutil
18
19 def getTimeStamp( ):
20 return time.strftime('%d%m%Y-%H%M%S')
21
22
23 class Match( object ):
24 '''
25 record where two genomes line up. stores only alignments for one part of the genome
26 '''
27 def __init__( self, start, end, seqID ):
28 self.seqID = seqID
29 self.start = start
30 self.end = end
31
32 def __repr__( self ):
33 return "Start: {0}, End:{1}, SeqID:{2}".format( self.start, self.end, self.seqID )
34
35 class PrimerSet( object ):
36
37 def __init__( self, id ):
38 self.id = id
39 self.productSize = 0
40 self.forwardPrimer = ""
41 self.forwardMeltTemp = ""
42 self.reversePrimer = ""
43 self.reverseMeltTemp = ""
44
45
46 def setProductSize( self, productSize):
47 self.productSize = productSize
48
49 def setForwardPrimerData( self, sequence, temp ):
50 self.forwardPrimer = sequence
51 self.forwardMeltTemp = temp
52
53 def setReversePrimerData( self, sequence, temp):
54 self.reversePrimer = sequence
55 self.reverseMeltTemp = temp
56
57
58 #search function from http://code.activestate.com/recipes/52224-find-a-file-given-a-search-path/
59 def search_file( filename ):
60 """ find file
61 """
62 search_path = os.getenv( 'PATH' )
63 logMessage( "utils::search_file", "Path: {0}".format( search_path ) )
64 file_found = 0
65 paths = split( search_path, pathsep )
66 for path in paths:
67 if os.path.exists( os.path.join( path, filename ) ):
68 file_found = 1
69 break
70 if file_found:
71 return os.path.abspath( os.path.join( path, filename ) )
72 else:
73 return None
74
75 tempDir = ""
76 removeTemp = True
77
78 verbose = False
79
80
81 def initialize( isVerbose, cleanup, lf): ##Mau: added lf
82 global removeTemp
83 global tempDir
84 global verbose
85 global logFile ##Mau: added logFile variable
86
87 logFile = lf #:Mau add line
88
89 verbose = isVerbose
90 tempDir = tempfile.mkdtemp( dir="" )
91 initializeLogging()
92 removeTemp = cleanup
93 logMessage( "utils::Initialize( )", "Initialization complete. Temporary directory: {0}".format( tempDir ) )
94
95 logFile = None
96
97
98 def printProgressMessage( message ):
99 global verbose
100 if verbose == True:
101 print message
102
103 def getTemporaryDirectory( ):
104 global tempDir
105 return tempDir
106
107 def initializeLogging():
108 global logFile
109 #logFileName = "uniqprimer_{0}.log".format( getTimeStamp( ) )
110 #logFileName = "log_uniqprimer.txt" ##Mau: commented out
111 logFileName = logFile ##Mau: changed
112 logFile = open( logFileName, 'w' )
113
114 def shutdown( ):
115 global removeTemp
116 global tempDir
117 shutdownLogging( )
118 if removeTemp == True:
119 print "*** Removing temporary directory ***"
120 shutil.rmtree( tempDir )
121
122 def shutdownLogging( ):
123 global logFile
124 if logFile != None:
125 logFile.close( )
126
127 def logList( method, list ):
128
129 message = reduce( lambda x,y: str( x ) + " " + str( y ) , list )
130 logMessage(method, message)
131
132
133 def logMessage( method, message ):
134 global logFile
135 if logFile == None:
136 return
137 log = "{0} - {1}".format( method, message )
138
139 logFile.write( log + "\n" )
140 logFile.flush( )
141
142 class EPrimerOptions( object ):
143
144 def __init__( self ):
145
146 self.minPrimerSize = 18
147 self.maxPrimerSize = 27
148 self.primerSize = 20
149 self.productRange = "200-250"
150
151 def setPrimerSize( self, size ):
152
153 size = int( size )
154 if size > 35:
155 size = 35
156
157 self.primerSize = size
158 if self.primerSize < self.minPrimerSize:
159 self.maxPrimerSize = self.primerSize
160 elif self.primerSize > self.maxPrimerSize:
161 self.maxPrimerSize = self.primerSize
162
163 def getPrimerSize( self ):
164 return self.primerSize
165
166 def setMinPrimerSize( self, minSize):
167 self.minPrimerSize = minSize
168
169 def getMinPrimerSize( self ):
170 return self.minPrimerSize
171
172 def setMaxPrimerSize( self, size ):
173 self.maxPrimerSize = size
174
175 def getMaxPrimerSize( self ):
176 return self.maxPrimerSize
177
178 def setProductRange( self, range ):
179 self.productRange = range
180
181 def getProductRange( self ):
182 return self.productRange
183
184 class NoPrimersExistException( exceptions.BaseException ):
185
186 def __init__( self ):
187 exceptions.BaseException( self )
188
189 class ProgramNotFoundException( exceptions.BaseException ):
190
191 def __init__( self, programName, details ):
192 exceptions.BaseException.__init__(self)
193 self.programName = programName
194 self.details = details
195
196 class NoFileFoundException( exceptions.BaseException ):
197
198 def __init__( self, filename ):
199 exceptions.BaseException.__init__(self)
200 self.filename = filename
201
202
203 class ModuleNotInitializedException( exceptions.BaseException ):
204
205 def __init__( self, moduleName, reason ):
206 self.moduleName = moduleName
207 self.reason = reason