Mercurial > repos > dereeper > uniqprimer
comparison uniqprimer-0.5.0/build/scripts-2.6/uniqprimer.py @ 3:3249d78ecfc2 draft
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author | dereeper |
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date | Mon, 03 Jan 2022 09:56:55 +0000 |
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2:7e0438dad4e9 | 3:3249d78ecfc2 |
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1 #!/SATA/bioinfo/galaxy/galaxy_env/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 Mau added the -o primerOutfile -l logfile option | |
11 ''' | |
12 | |
13 import exceptions | |
14 import sys | |
15 import time | |
16 | |
17 import getopt | |
18 from primertools import * | |
19 | |
20 version="0.5.0" | |
21 | |
22 | |
23 class UniqPrimerFinder( object ): | |
24 | |
25 def __init__( self, includeFiles, excludeFiles, crossValidate, eprimerOptions): | |
26 | |
27 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder" ) | |
28 self.includeFiles = includeFiles | |
29 self.includeFileManager = includefilemanager.IncludeFileManager( ) | |
30 | |
31 self.excludeFiles = excludeFiles | |
32 self.excludeFileManager= excludefilemanager.ExcludeFileManager( ) | |
33 | |
34 self.primerManager = primermanager.PrimerManager( eprimerOptions ) | |
35 | |
36 self.crossValidate = crossValidate | |
37 | |
38 | |
39 utils.logMessage( "UniqPrimerFinder::__init__()", "Initializing UniqPrimerFinder - complete" ) | |
40 | |
41 def writeOutputFile( self, primers, outputFileName, maxresults = 100 ): | |
42 ''' | |
43 primers: a list of PrimerSet obs | |
44 ''' | |
45 ##outputFileName = uPrimer ##Mau: defined this.. | |
46 outputFile = open( outputFileName, 'w' ) | |
47 | |
48 i = 0 | |
49 for primer in primers: | |
50 i += 1 | |
51 | |
52 outputFile.write( "{0}\t{1}\t{2}\t{3}\n".format( i, primer.forwardPrimer, primer.reversePrimer, primer.productSize ) ) | |
53 | |
54 if i > maxresults: | |
55 break | |
56 | |
57 utils.logMessage( "UniqPrimerFinder::writeOutputFile()", "output file written." ) | |
58 | |
59 | |
60 def findPrimers( self, outputFile = "uPrimer.txt" ): | |
61 outputFile = uPrimer ## Mau adds to overwrite the above value | |
62 | |
63 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finding primers for include files" ) | |
64 startTime = time.time( ) | |
65 #generate the combined sequence fasta file for all exclude sequences | |
66 utils.printProgressMessage( "*** Creating Combined Fasta File for Exclude Files ***" ) | |
67 for excludeFile in self.excludeFiles: | |
68 self.excludeFileManager.addExcludeFile( excludeFile ) | |
69 | |
70 self.excludeFileManager.exportSequences( ) | |
71 | |
72 self.includeFileManager.setExcludeFile( self.excludeFileManager.getOutputFileName( ) ) | |
73 | |
74 utils.printProgressMessage( "*** Finding Sequences Unique to Target Genome ***" ) | |
75 | |
76 #run nucmer program on all include files | |
77 for includeFile in self.includeFiles: | |
78 self.includeFileManager.processIncludeFile( includeFile ) | |
79 | |
80 #get the sequences found in include files, but no the exclude file. | |
81 uniqueSequences = self.includeFileManager.getUniqueSequences( ) | |
82 | |
83 utils.printProgressMessage( "*** Finding Primers ***" ) | |
84 | |
85 primers = self.primerManager.getPrimers( uniqueSequences ) | |
86 | |
87 if self.crossValidate == True: | |
88 utils.printProgressMessage( "*** Cross Validating Primers ***" ) | |
89 primers = self.primerManager.crossValidatePrimers( primers, self.excludeFileManager.getOutputFileName( ) ) | |
90 | |
91 | |
92 utils.logMessage( "UniqPrimerFinder::findPrimers( )", "found {0} unique sequences".format( len( primers ) ) ) | |
93 | |
94 self.writeOutputFile( primers, outputFile ) | |
95 | |
96 utils.logMessage( "UniqPrimerFinder::findPrimers()", "Finished finding primers" ) | |
97 endTime = time.time() | |
98 elapsedMinutes = int( ( endTime - startTime ) / 60 ) | |
99 elapsedSeconds = int( ( endTime - startTime ) % 60 ) | |
100 print "*** Time Elapsed: {0} minutes, {1} seconds ***".format( elapsedMinutes, elapsedSeconds ) | |
101 print "*** Output Written to {0} ***".format( outputFile ) | |
102 | |
103 | |
104 def printUsageAndQuit( ): | |
105 global version | |
106 print "uniqprimer - finds primers unique to a genome" | |
107 print "Version: " + str( version ) | |
108 print "Summary of Options." | |
109 print "Required Arguments:" | |
110 print " -i <filename>: use <filename> as an include file. Primers will be identified for this genome" | |
111 print " -x <filename>: use <filename> as an exclude file. Primers for this genome will be excluded" | |
112 print " -o <filename>: specify the name of the unique primer output file (default is uPrimer.txt)" ## Mau added.. | |
113 print " -l <filename>: specify the name of the log output file" ## Mau added.. | |
114 | |
115 print "\nOptional Arguments:" | |
116 print " --productsizerage: set a range for the desired size of PCR product (default=200-250). Example: ./uniqprimer -productsizerage 100-150" | |
117 print " --primersize: set the desired primer size (default=20)" | |
118 print " --minprimersize: set the minimum primer size (default=27)" | |
119 print " --maxprimersize: set the maximum primer size (default=18)" | |
120 print " --crossvalidate: force the program to cross validate primers against exclude files for extra certainty" | |
121 print " --keeptempfiles: force the program to keep temporary files" | |
122 | |
123 print "\n\nExample:" | |
124 print "uniqprimer -i <includefile1> -i <includefile2> ... -i <includefileN> -x <excludefile1> -x <excludefile2> ... -x <excludefileN> -o primers.txt -l logfile.txt" | |
125 utils.shutdownLogging( ) | |
126 sys.exit( ) | |
127 | |
128 | |
129 opts = 'i:x:h:o:l:' # Mau added :o & :l for outfile specification | |
130 longopts=[ "productsizerange=", "primersize=", "minprimersize=", "maxprimersize=", "crossvalidate", "keeptempfiles" ] | |
131 | |
132 def parseArgs( args ): | |
133 | |
134 | |
135 global uPrimer ## Mau added lf, brute force... | |
136 global lf # Mau added lf, brute force... | |
137 #uPrimer = "uPrimer.txt" ##the default value... | |
138 | |
139 crossValidate = False | |
140 cleanup = True | |
141 optlist, args = getopt.getopt( args, opts, longopts ) | |
142 | |
143 includeFiles = [ ] | |
144 excludeFiles = [ ] | |
145 eprimerOptions = utils.EPrimerOptions( ) | |
146 | |
147 verbose = False | |
148 for opt in optlist: | |
149 if opt[ 0 ] == '-i': | |
150 includeFiles.append( opt[ 1 ] ) | |
151 elif opt[ 0 ] == '-x': | |
152 excludeFiles.append( opt[ 1] ) | |
153 elif opt[ 0 ] == '-v': | |
154 verbose = True | |
155 elif opt[ 0 ] == '-o': ## Mau added, if -o... | |
156 uPrimer = str(opt[1]) ## Mau added, then get filename for outfile after -o | |
157 elif opt[ 0 ] == '-l': ## Mau added, if -l... | |
158 lf = str(opt[1]) ## Mau added, then get filename for logfile after -l | |
159 elif opt[ 0 ] == '--productsizerange': | |
160 eprimerOptions.setProductRange( opt[ 1 ] ) | |
161 productsizerange = opt[ 1 ] | |
162 elif opt[ 0 ] == '--primersize': | |
163 eprimerOptions.setPrimerSize( opt[1 ] ) | |
164 elif opt[ 0 ] == '--minprimersize': | |
165 eprimerOptions.setMinPrimerSize( opt[1 ] ) | |
166 elif opt[ 0 ] == '--maxprimersize': | |
167 eprimerOptions.setMaxPrimerSize( opt[1 ] ) | |
168 elif opt[ 0 ] == '--crossvalidate': | |
169 crossValidate = True | |
170 elif opt[ 0 ] == '--crossvalidate': | |
171 crossValidate = True | |
172 elif opt[ 0 ] == '--keeptempfiles': | |
173 cleanup = False | |
174 elif opt[ 0 ] == '-h': | |
175 printUsageAndQuit( ) | |
176 else: | |
177 print "Unknown option: " + str( opt[ 0 ] ) | |
178 printUsageAndQuit( ) | |
179 #print "uPrimer: " + uPrimer + " log file name: " + lf + "\n" | |
180 if len( includeFiles ) == 0 or len( excludeFiles ) == 0: | |
181 | |
182 print "You must specify at least one include file and at least one exclude file" | |
183 printUsageAndQuit( ) | |
184 | |
185 return includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf , uPrimer #Mau: add lf, uPrime | |
186 | |
187 def main( args, debug = False): | |
188 #parse the command line arguments for include and exclude files | |
189 | |
190 includeFiles, excludeFiles, crossValidate, cleanup, verbose, eprimerOptions, lf, uPrimer = parseArgs( args ) ##Mau add: lf | |
191 | |
192 utils.initialize( True, cleanup, lf) ##Mau: add lf | |
193 | |
194 #find primers for the include sequences | |
195 | |
196 try: | |
197 utils.logMessage( "uniqprimer::Main( )", "Logging include files: " ) | |
198 utils.logList( "uniqprimer::Main( )", includeFiles ) | |
199 utils.logMessage( "uniqprimer::Main( )", "Logging exclude files: " ) | |
200 utils.logList( "uniqprimer::Main( )", excludeFiles) | |
201 print "*** Finding Primers ***" | |
202 uniqPrimer = UniqPrimerFinder( includeFiles, excludeFiles, crossValidate, eprimerOptions) | |
203 uniqPrimer.findPrimers( ) | |
204 except utils.NoFileFoundException as nfe: | |
205 print "File not found: " + str( nfe.filename ) | |
206 printUsageAndQuit( ) | |
207 except utils.ProgramNotFoundException as pnfe: | |
208 print str( pnfe.programName ) + ": program is not installed or is not in your path." | |
209 print str( pnfe.details ) | |
210 except utils.NoPrimersExistException as npe: | |
211 print "Failure: No unique primers exist for this combination" | |
212 except exceptions.BaseException as e: | |
213 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!" | |
214 print "Details:" | |
215 print e | |
216 | |
217 utils.shutdown( ) | |
218 | |
219 print "*** Finished ***" | |
220 | |
221 if __name__ == '__main__': | |
222 | |
223 #temp_args = "-i data/testdata/smallinclude.ffn -x data/testdata/smallexclude.ffn".split( ) | |
224 | |
225 #temp_args = "-i data/XOO_MAI1_scaffolds.fas -x data/KACC.ffn".split( ) | |
226 if len( sys.argv ) == 1: | |
227 printUsageAndQuit( ) | |
228 main( sys.argv[ 1: ], debug = True ) | |
229 | |
230 | |
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