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comparison uniqprimer-0.5.0/uniqprimer.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 #!/usr/bin/python
2
3 '''
4 Created on Jan 1, 2011
5
6 @author: John L. Herndon
7 @contact: herndon@cs.colostate.edu
8 @organization: Colorado State University
9 @group: Computer Science Department, Asa Ben-Hur's laboratory
10 '''
11
12 import exceptions
13 import sys
14 import time
15 import os ## added by Alexis
16
17 sys.path.append("/gs7k1/home/galaxy/galaxy_env/lib/python2.7/site-packages")
18
19 import getopt
20 from primertools import *
21
22 version="0.5.0"
23
24
25 class UniqPrimerFinder( object ):
26
27 def __init__( self, includeFiles, excludeFiles, crossValidate, eprimerOptions):
28
29 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder" )
30 self.includeFiles = includeFiles
31 self.includeFileManager = includefilemanager.IncludeFileManager( )
32
33 self.excludeFiles = excludeFiles
34 self.excludeFileManager= excludefilemanager.ExcludeFileManager( )
35
36 self.primerManager = primermanager.PrimerManager( eprimerOptions )
37
38 self.crossValidate = crossValidate
39
40
41 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder - complete" )
42
43 def writeOutputFile( self, primers, outputFileName, maxresults = 100 ):
44 '''
45 primers: a list of PrimerSet obs
46 '''
47 ##outputFileName = uPrimer ##Mau: defined this..
48 outputFile = open( outputFileName, 'w' )
49
50 i = 0
51 for primer in primers:
52 i += 1
53
54 outputFile.write( "{0}\t{1}\t{2}\t{3}\n".format( i, primer.forwardPrimer, primer.reversePrimer, primer.productSize ) )
55
56 if i > maxresults:
57 break
58
59 utils.logMessage( "UniqPrimerFinder::writeOutputFile()", "output file written." )
60
61
62 def findPrimers( self, outputFile = "uPrimer.txt" ):
63 outputFile = uPrimer ## Mau adds to overwrite the above value
64
65
66 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finding primers for include files" )
67 startTime = time.time( )
68 #generate the combined sequence fasta file for all exclude sequences
69 utils.printProgressMessage( "*** Creating Combined Fasta File for Exclude Files ***" )
70 for excludeFile in self.excludeFiles:
71 self.excludeFileManager.addExcludeFile( excludeFile )
72
73 self.excludeFileManager.exportSequences( )
74
75 self.includeFileManager.setExcludeFile( self.excludeFileManager.getOutputFileName( ) )
76
77 utils.printProgressMessage( "*** Finding Sequences Unique to Target Genome ***" )
78
79 #run nucmer program on all include files
80 for includeFile in self.includeFiles:
81 self.includeFileManager.processIncludeFile( includeFile )
82
83 #get the sequences found in include files, but no the exclude file.
84 uniqueSequences = self.includeFileManager.getUniqueSequences( )
85
86 utils.printProgressMessage( "*** Finding Primers ***" )
87
88 primers = self.primerManager.getPrimers( uniqueSequences )
89
90 if self.crossValidate == True:
91 utils.printProgressMessage( "*** Cross Validating Primers ***" )
92 primers = self.primerManager.crossValidatePrimers( primers, self.excludeFileManager.getOutputFileName( ) )
93 # added by Alexis, primersearch also against all include files
94 #run primersearch program on all include files
95 j=0
96 for includeFile in self.includeFiles: # added by Alexis
97 j = j + 1
98 primers = self.primerManager.crossValidatePrimers2( primers, includeFile, j) # added by Alexis
99
100
101 utils.logMessage( "UniqPrimerFinder::findPrimers( )", "found {0} unique sequences".format( len( primers ) ) )
102
103 self.writeOutputFile( primers, outputFile )
104
105 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finished finding primers" )
106 endTime = time.time()
107 elapsedMinutes = int( ( endTime - startTime ) / 60 )
108 elapsedSeconds = int( ( endTime - startTime ) % 60 )
109 print "*** Time Elapsed: {0} minutes, {1} seconds ***".format( elapsedMinutes, elapsedSeconds )
110 print "*** Output Written to {0} ***".format( outputFile )
111
112
113 def printUsageAndQuit( ):
114 global version
115 print "uniqprimer - finds primers unique to a genome"
116 print "Version: " + str( version )
117 print "Summary of Options."
118 print "Required Arguments:"
119 print " -i <filename>: use <filename> as an include file. Primers will be identified for this genome"
120 print " -x <filename>: use <filename> as an exclude file. Primers for this genome will be excluded"
121 print " -o <filename>: specify the name of the unique primer output file (default is uPrimer.txt)" ## Mau added..
122 print " -l <filename>: specify the name of the log output file" ## Mau added..
123 print " -f <filename>: specify the name of the Fasta of differential sequences" ## Alexis added..
124
125 print "\nOptional Arguments:"
126 print " --productsizerage: set a range for the desired size of PCR product (default=200-250). Example: ./uniqprimer -productsizerage 100-150"
127 print " --primersize: set the desired primer size (default=20)"
128 print " --minprimersize: set the minimum primer size (default=27)"
129 print " --maxprimersize: set the maximum primer size (default=18)"
130 print " --crossvalidate: force the program to cross validate primers against exclude files for extra certainty"
131 print " --keeptempfiles: force the program to keep temporary files"
132
133 print "\n\nExample:"
134 print "uniqprimer -i <includefile1> -i <includefile2> ... -i <includefileN> -x <excludefile1> -x <excludefile2> ... -x <excludefileN> -o primers.txt -l logfile.txt -f seqForPrimer3.fa"
135 utils.shutdownLogging( )
136 sys.exit( )
137
138
139 opts = 'i:x:h:o:l:f:' # Mau added :o & :l for outfile specification, Alexis added :f
140 longopts=[ "productsizerange=", "primersize=", "minprimersize=", "maxprimersize=", "crossvalidate", "keeptempfiles" ]
141
142 def parseArgs( args ):
143
144
145 global uPrimer ## Mau added lf, brute force...
146 global lf # Mau added lf, brute force...
147 global fastaDiff # Alexis added fastaDiff
148 #uPrimer = "uPrimer.txt" ##the default value...
149
150 crossValidate = False
151 cleanup = True
152 optlist, args = getopt.getopt( args, opts, longopts )
153
154 includeFiles = [ ]
155 excludeFiles = [ ]
156 eprimerOptions = utils.EPrimerOptions( )
157
158 verbose = False
159 for opt in optlist:
160 if opt[ 0 ] == '-i':
161 includeFiles.append( opt[ 1 ] )
162 elif opt[ 0 ] == '-x':
163 excludeFiles.append( opt[ 1] )
164 elif opt[ 0 ] == '-v':
165 verbose = True
166 elif opt[ 0 ] == '-o': ## Mau added, if -o...
167 uPrimer = str(opt[1]) ## Mau added, then get filename for outfile after -o
168 elif opt[ 0 ] == '-l': ## Mau added, if -l...
169 lf = str(opt[1]) ## Mau added, then get filename for logfile after -l
170 elif opt[ 0 ] == '-f': ## Alexis added, if -f
171 fastaDiff = str(opt[1]) ## Alexis added, then get filename for fasta file after -f
172 elif opt[ 0 ] == '--productsizerange':
173 eprimerOptions.setProductRange( opt[ 1 ] )
174 productsizerange = opt[ 1 ]
175 elif opt[ 0 ] == '--primersize':
176 eprimerOptions.setPrimerSize( opt[1 ] )
177 elif opt[ 0 ] == '--minprimersize':
178 eprimerOptions.setMinPrimerSize( opt[1 ] )
179 elif opt[ 0 ] == '--maxprimersize':
180 eprimerOptions.setMaxPrimerSize( opt[1 ] )
181 elif opt[ 0 ] == '--crossvalidate':
182 crossValidate = True
183 elif opt[ 0 ] == '--crossvalidate':
184 crossValidate = True
185 elif opt[ 0 ] == '--keeptempfiles':
186 cleanup = False
187 elif opt[ 0 ] == '-h':
188 printUsageAndQuit( )
189 else:
190 print "Unknown option: " + str( opt[ 0 ] )
191 printUsageAndQuit( )
192 #print "uPrimer: " + uPrimer + " log file name: " + lf + "\n"
193 if len( includeFiles ) == 0 or len( excludeFiles ) == 0:
194
195 print "You must specify at least one include file and at least one exclude file"
196 printUsageAndQuit( )
197
198 return includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf , uPrimer, fastaDiff #Mau: add lf, uPrime
199
200 def main( args, debug = False):
201 #parse the command line arguments for include and exclude files
202
203 includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf, uPrimer, fastaDiff = parseArgs( args ) ##Mau add: lf
204 utils.initialize( True, cleanup, lf) ##Mau: add lf
205 #find primers for the include sequences
206
207 tmpdir = utils.getTemporaryDirectory() ## added by Alexis
208 command = "cp -rf " + tmpdir + "/sequenceForEprimer.fasta" + " " + fastaDiff
209
210 try:
211 utils.logMessage( "uniqprimer::Main( )", "Logging include files: " )
212 utils.logList( "uniqprimer::Main( )", includeFiles )
213 utils.logMessage( "uniqprimer::Main( )", "Logging exclude files: " )
214 utils.logList( "uniqprimer::Main( )", excludeFiles)
215 print "*** Finding Primers ***"
216 uniqPrimer = UniqPrimerFinder( includeFiles, excludeFiles, crossValidate, eprimerOptions)
217 uniqPrimer.findPrimers( )
218 except utils.NoFileFoundException as nfe:
219 print "File not found: " + str( nfe.filename )
220 printUsageAndQuit( )
221 except utils.ProgramNotFoundException as pnfe:
222 print str( pnfe.programName ) + ": program is not installed or is not in your path."
223 print str( pnfe.details )
224 except utils.NoPrimersExistException as npe:
225 print "Failure: No unique primers exist for this combination"
226 except exceptions.BaseException as e:
227 print "It appears that an unknown sequence of events has resulted in the internal explosion of this program. Please send the file called \'log_uniqprimer.txt\' to herndon@cs.colostate.edu and tell that bonehead John to fix it!"
228 print "Details:"
229 print e
230
231 os.system("cp -rf " + tmpdir + "/sequenceForEprimer.fasta" + " " + fastaDiff)
232 utils.shutdown( )
233
234 print "*** Finished ***"
235
236 if __name__ == '__main__':
237
238 #temp_args = "-i data/testdata/smallinclude.ffn -x data/testdata/smallexclude.ffn".split( )
239
240 #temp_args = "-i data/XOO_MAI1_scaffolds.fas -x data/KACC.ffn".split( )
241 if len( sys.argv ) == 1:
242 printUsageAndQuit( )
243 main( sys.argv[ 1: ], debug = True )
244
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