|
0
|
1 #!/usr/bin/env python
|
|
|
2
|
|
|
3
|
|
|
4 import os
|
|
|
5 import sys
|
|
|
6 import time
|
|
|
7 import glob
|
|
|
8 import shutil
|
|
|
9 import ConfigParser
|
|
|
10 from commons.core.seq.FastaUtils import *
|
|
|
11 import operator
|
|
|
12 import re
|
|
|
13
|
|
|
14
|
|
|
15
|
|
|
16 if not "REPET_PATH" in os.environ.keys():
|
|
|
17 print "ERROR: no environment variable REPET_PATH"
|
|
|
18 sys.exit(1)
|
|
|
19
|
|
|
20 if (not "REPET_DB" in os.environ.keys()) or (not "REPET_HOST" in os.environ.keys()) or (not "REPET_PORT" in os.environ.keys()) or (not "REPET_USER" in os.environ.keys()) or (not "REPET_PW" in os.environ.keys()):
|
|
|
21 print "ERROR: there is at least one environment database variable missing : REPET_DB, REPET_PORT, REPET_HOST, REPET_USER or REPET_PW"
|
|
|
22 sys.exit(1)
|
|
|
23
|
|
|
24 if not "REPET_JOB_MANAGER" in os.environ.keys():
|
|
|
25 print "ERROR: no environment variable REPET_JOB_MANAGER"
|
|
|
26 sys.exit(1)
|
|
|
27
|
|
|
28
|
|
|
29 if not "%s/bin" % os.environ["REPET_PATH"] in os.environ["PATH"]:
|
|
|
30 os.environ["PATH"] = "%s/bin:%s" % (os.environ["REPET_PATH"], os.environ["PATH"])
|
|
|
31
|
|
|
32 sys.path.append(os.environ["REPET_PATH"])
|
|
|
33 if not "PYTHONPATH" in os.environ.keys():
|
|
|
34 os.environ["PYTHONPATH"] = os.environ["REPET_PATH"]
|
|
|
35 else:
|
|
|
36 os.environ["PYTHONPATH"] = "%s:%s" % (os.environ["REPET_PATH"], os.environ["PYTHONPATH"])
|
|
|
37
|
|
|
38 from commons.core.LoggerFactory import LoggerFactory
|
|
|
39 from commons.core.checker.RepetException import RepetException
|
|
|
40 from commons.core.utils.FileUtils import FileUtils
|
|
|
41 from commons.core.utils.RepetOptionParser import RepetOptionParser
|
|
|
42 from commons.core.seq.FastaUtils import FastaUtils
|
|
|
43 from commons.core.sql.DbFactory import DbFactory
|
|
|
44 from itertools import islice
|
|
|
45
|
|
|
46 LOG_DEPTH = "TEdenovo.pipeline"
|
|
|
47
|
|
|
48 class TEdenovo_lite(object):
|
|
|
49
|
|
|
50 def __init__(self, configFileName = "", fastaFileName = "", verbosity = 0):
|
|
|
51 self._configFileName = configFileName
|
|
|
52 self._fastaFileName = os.path.abspath(fastaFileName)
|
|
|
53 self._projectName = time.strftime("%Y%m%d%H%M%S")
|
|
|
54 self._limitSeqSize = 200000000
|
|
|
55
|
|
|
56 if "REPET_NUCL_BANK" in os.environ.keys():
|
|
|
57 if os.path.exists(os.environ["REPET_NUCL_BANK"]):
|
|
|
58 self._nucl_bank = os.environ["REPET_NUCL_BANK"]
|
|
|
59 else :
|
|
|
60 print "ERROR : the nucleotides bank configured doesn't exist. Please correct it in the REPET_NUCL_BANK variable"
|
|
|
61 sys.exit(1)
|
|
|
62 else :
|
|
|
63 self._nucl_bank = ""
|
|
|
64 if "REPET_PROT_BANK" in os.environ.keys():
|
|
|
65 if os.path.exists(os.environ["REPET_PROT_BANK"]):
|
|
|
66 self._prot_bank = os.environ["REPET_PROT_BANK"]
|
|
|
67 else :
|
|
|
68 print "ERROR : the proteins bank configured doesn't exist. Please correct it in the REPET_PROT_BANK variable"
|
|
|
69 sys.exit(1)
|
|
|
70 else :
|
|
|
71 self._prot_bank = ""
|
|
|
72 if "REPET_HMM_PROFILES" in os.environ.keys():
|
|
|
73 if os.path.exists(os.environ["REPET_HMM_PROFILES"]):
|
|
|
74 self._HMM_profiles = os.environ["REPET_HMM_PROFILES"]
|
|
|
75 else :
|
|
|
76 print "ERROR : the hmm profiles bank configured doesn't exist. Please correct it in the REPET_HMM_PROFILES variable"
|
|
|
77 sys.exit(1)
|
|
|
78 else :
|
|
|
79 self._HMM_profiles = ""
|
|
|
80 if "REPET_RDNA_BANK" in os.environ.keys():
|
|
|
81 if os.path.exists(os.environ["REPET_RDNA_BANK"]):
|
|
|
82 self._rdna_bank = os.environ["REPET_RDNA_BANK"]
|
|
|
83 else :
|
|
|
84 print "ERROR : the rDNA bank configured doesn't exist. Please correct it in the REPET_PROT_BANK variable"
|
|
|
85 sys.exit(1)
|
|
|
86 else :
|
|
|
87 self._rdna_bank = ""
|
|
|
88 if self._nucl_bank == "" and self._prot_bank == "" and self._HMM_profiles == "" and self._rdna_bank == "" :
|
|
|
89 print "WARNING : No bank are configured ... To set banks please add REPET_NUCL_BANK, REPET_PROT_BANK, REPET_HMM_PROFILES and/or REPET_RDNA_BANK in your environment"
|
|
|
90 if "REPET_TMP_DIR" in os.environ.keys():
|
|
|
91 self._tmp_dir = os.environ["REPET_TMP_DIR"]
|
|
|
92 else :
|
|
|
93 self._tmp_dir = ""
|
|
|
94 self._outputFasta = ""
|
|
|
95 self._classif = False
|
|
|
96 self._outputClassif = ""
|
|
|
97 self._outputStats = ""
|
|
|
98 self._verbosity = verbosity
|
|
|
99 self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
|
|
|
100
|
|
|
101 def setAttributesFromCommandLine(self):
|
|
|
102 description = "This script is a ligth version of TEdenovo. It writes configuration file and launches TEdenovo."
|
|
|
103 epilog = "Example: TEdenovo_lite.py -i fastaFileName \n"
|
|
|
104 version = "2.0"
|
|
|
105 parser = RepetOptionParser(description = description, epilog = epilog, version = version)
|
|
|
106 parser.add_option("-i", "--fasta", dest = "fastaFileName" , action = "store" , type = "string", help ="input fasta file name ", default = "")
|
|
|
107 parser.add_option("-c", "--withClassif", dest="withClassif", action="store_true", help = " Get classification files in output.", default = False)
|
|
|
108 parser.add_option("-o", "--output", dest="outputLabel" , action = "store", type = "string", help = "[optional] Prefix label for output file(s).", default = "")
|
|
|
109 parser.add_option("-v", "--verbosity", dest = "verbosity", action = "store", type = "int", help = "Verbosity [optional] [default: 2]", default = 2)
|
|
|
110 options = parser.parse_args()[0]
|
|
|
111 self._setAttributesFromOptions(options)
|
|
|
112
|
|
|
113 def _setAttributesFromOptions(self, options):
|
|
|
114 self.setConfigFileName("")
|
|
|
115 if options.fastaFileName=="":
|
|
|
116 print "ERROR : You have to enter an input fasta file"
|
|
|
117 print "Example: TEdenovo_lite.py -i fastaFileName \n"
|
|
|
118 print "More option : TEdenovo_lite.py --help "
|
|
|
119 exit(1)
|
|
|
120 else :
|
|
|
121 self._fastaFileName = os.path.abspath(options.fastaFileName)
|
|
|
122 if options.outputLabel=="":
|
|
|
123 fastaBaseName=os.path.abspath(re.search(r'([^\/\\]*)\.[fa|fasta|fsa|fas]',options.fastaFileName).groups()[0])
|
|
|
124 options.outputLabel=fastaBaseName
|
|
|
125 self._outputFasta = os.path.abspath(options.outputLabel+"-%s-denovoLibTEs_filtered.fa"%self._projectName[:8])
|
|
|
126 self._outputStats = os.path.abspath(options.outputLabel+"-%s-classif_stats.txt"%self._projectName[:8])
|
|
|
127 self._verbosity = options.verbosity
|
|
|
128 if options.withClassif :
|
|
|
129 self._classif=True
|
|
|
130 self._outputClassif = os.path.abspath(options.outputLabel+'-%s.classif'%self._projectName[:8])
|
|
|
131
|
|
|
132 def setConfigFileName(self, configFileName):
|
|
|
133 self._configFileName = configFileName
|
|
|
134 if not self._configFileName:
|
|
|
135 self._configFileName = "TEdenovo_Galaxy_config_%s" % self._projectName
|
|
|
136
|
|
|
137 def setAttributesFromConfigFile(self, configFileName):
|
|
|
138 config = ConfigParser.ConfigParser()
|
|
|
139 config.readfp( open(configFileName) )
|
|
|
140
|
|
|
141
|
|
|
142 def _writeConfigFile(self):
|
|
|
143 if FileUtils.isRessourceExists(self._configFileName):
|
|
|
144 self._logAndRaise("Configuration file '%s' already exists. Won't be overwritten.")
|
|
|
145
|
|
|
146 shutil.copy("%s/config/TEdenovo.cfg" % os.environ.get("REPET_PATH"), self._configFileName)
|
|
|
147 self.setAttributesFromConfigFile(self._configFileName)
|
|
|
148
|
|
|
149 os.system("sed -i 's|repet_host: <your_MySQL_host>|repet_host: %s|' %s" % (os.environ["REPET_HOST"], self._configFileName))
|
|
|
150 os.system("sed -i 's|repet_user: <your_MySQL_login>|repet_user: %s|' %s" % (os.environ["REPET_USER"], self._configFileName))
|
|
|
151 os.system("sed -i 's|repet_pw: <your_MySQL_password>|repet_pw: %s|' %s" % (os.environ["REPET_PW"], self._configFileName))
|
|
|
152 os.system("sed -i 's|repet_db: <your_MySQL_db>|repet_db: %s|' %s" % (os.environ["REPET_DB"], self._configFileName))
|
|
|
153 os.system("sed -i 's|repet_port: 3306|repet_port: %s|' %s" % (os.environ["REPET_PORT"], self._configFileName))
|
|
|
154 os.system("sed -i 's|repet_job_manager: SGE|repet_job_manager: %s|' %s" % (os.environ["REPET_JOB_MANAGER"], self._configFileName))
|
|
|
155 os.system("sed -i 's|project_name: <your_project_name>|project_name: %s|' %s" % (self._projectName, self._configFileName))
|
|
|
156 os.system("sed -i 's|project_dir: <absolute_path_to_your_project_directory>|project_dir: %s|' %s" % (os.getcwd().replace("/", "\/"), self._configFileName))
|
|
|
157 os.system("sed -i 's|tmpDir:|tmpDir: %s|g' %s" % (self._tmp_dir, self._configFileName))
|
|
|
158
|
|
|
159 if self._nucl_bank != "" and self._nucl_bank != None:
|
|
|
160 os.system("sed -i 's|TE_BLRn: no|TE_BLRn: yes|' %s" % self._configFileName)
|
|
|
161 os.system("sed -i 's|TE_BLRtx: no|TE_BLRtx: yes|' %s" % self._configFileName)
|
|
|
162 os.system("sed -i 's|TE_nucl_bank: <bank_of_TE_nucleotide_sequences_such_as_Repbase>|TE_nucl_bank: %s|' %s" % (os.path.basename(self._nucl_bank), self._configFileName))
|
|
|
163
|
|
|
164 if self._prot_bank != "" and self._prot_bank != None:
|
|
|
165 os.system("sed -i 's|TE_BLRx: no|TE_BLRx: yes|' %s" % self._configFileName)
|
|
|
166 os.system("sed -i 's|TE_prot_bank: <bank_of_TE_amino-acid_sequences_such_as_Repbase>|TE_prot_bank: %s|' %s" % (os.path.basename(self._prot_bank), self._configFileName))
|
|
|
167
|
|
|
168 if self._HMM_profiles != "" and self._HMM_profiles != None:
|
|
|
169 os.system("sed -i 's|TE_HMMER: no|TE_HMMER: yes|' %s" % self._configFileName)
|
|
|
170 os.system("sed -i 's|TE_HMM_profiles: <bank_of_HMM_profiles>|TE_HMM_profiles: %s|' %s" % (os.path.basename(self._HMM_profiles),self._configFileName))
|
|
|
171
|
|
|
172 if self._rdna_bank != "" and self._rdna_bank != None:
|
|
|
173 os.system("sed -i 's|rDNA_BLRn: no|rDNA_BLRn: yes|' %s" % self._configFileName)
|
|
|
174 os.system("sed -i 's|rDNA_bank: <bank_of_rDNA_sequences_from_eukaryota>|rDNA_bank: %s|' %s" % (os.path.basename(self._rdna_bank),self._configFileName))
|
|
|
175
|
|
|
176 os.system("sed -i 's|filter_host_gene: no|filter_host_gene: yes|' %s" % (self._configFileName))
|
|
|
177
|
|
|
178
|
|
|
179 def removeNstretches(self,maxNstretchesSize=11,minContigsize=10000):
|
|
|
180 if self._verbosity > 0:
|
|
|
181 print "Removing Nstretches longer than %d pb and removing conting shorter than %d pb"%(maxNstretchesSize,minContigsize)
|
|
|
182 t0=time.time()
|
|
|
183 Nstretches=FastaUtils.getNstretchesRangesList(self._fastaFileName,maxNstretchesSize)
|
|
|
184 t1=time.time()
|
|
|
185 refBSDB = BioseqDB(self._fastaFileName)
|
|
|
186 t3=time.time()
|
|
|
187 debut=1
|
|
|
188 t2=time.time()
|
|
|
189 if len(Nstretches)>0:
|
|
|
190 currentchrom=Nstretches[0].seqname
|
|
|
191 refBS=refBSDB.fetch(currentchrom)
|
|
|
192 t3=time.time()
|
|
|
193 newBSDB = BioseqDB()
|
|
|
194 i=0
|
|
|
195 seqInNstretches = []
|
|
|
196 for Nstretch in Nstretches :
|
|
|
197 i+=1
|
|
|
198 tmpBS=""
|
|
|
199 if Nstretch.seqname not in seqInNstretches :
|
|
|
200 seqInNstretches.append(Nstretch.seqname)
|
|
|
201 if currentchrom==Nstretch.seqname:
|
|
|
202 fin=Nstretch.start-1
|
|
|
203 size=fin-debut+1
|
|
|
204 if size>minContigsize :
|
|
|
205 tmpBS=refBS.subseq(debut,fin)
|
|
|
206 newBSDB.add(tmpBS)
|
|
|
207
|
|
|
208 debut=Nstretch.end+1
|
|
|
209
|
|
|
210 else :
|
|
|
211 fin = refBSDB.getSeqLength(currentchrom)
|
|
|
212 size=fin-debut+1
|
|
|
213 if size>minContigsize :
|
|
|
214 tmpBS=refBS.subseq(debut,fin)
|
|
|
215 newBSDB.add(tmpBS)
|
|
|
216 currentchrom=Nstretch.seqname
|
|
|
217 refBS=refBSDB.fetch(currentchrom)
|
|
|
218 debut=1
|
|
|
219 fin==Nstretch.start
|
|
|
220 size=fin-debut+1
|
|
|
221 if size>minContigsize :
|
|
|
222 tmpBS=refBS.subseq(debut,fin)
|
|
|
223 newBSDB.add(tmpBS)
|
|
|
224 debut=Nstretch.end+1
|
|
|
225
|
|
|
226 if len(Nstretches)>0:
|
|
|
227 fin = refBSDB.getSeqLength(currentchrom)
|
|
|
228 size=fin-debut+1
|
|
|
229 if size>minContigsize :
|
|
|
230 tmpBS=refBS.subseq(debut,fin)
|
|
|
231 newBSDB.add(tmpBS)
|
|
|
232
|
|
|
233 for refName in refBSDB.getHeaderList() :
|
|
|
234 if refName not in seqInNstretches:
|
|
|
235 debut=1
|
|
|
236 fin=refBSDB.getSeqLength(refName)
|
|
|
237 size=fin-debut+1
|
|
|
238 if size>minContigsize :
|
|
|
239 refBS=refBSDB.fetch(refName)
|
|
|
240 tmpBS=refBS.subseq(debut,fin)
|
|
|
241 newBSDB.add(tmpBS)
|
|
|
242
|
|
|
243
|
|
|
244 t5b=time.time()
|
|
|
245 if self._verbosity >= 2:
|
|
|
246 print "%s contigs selected from %s scaffolds"%(newBSDB.getSize(),refBSDB.getSize())
|
|
|
247 #newBSDB.sortByLength(reverse=True)
|
|
|
248
|
|
|
249 return newBSDB
|
|
|
250
|
|
|
251
|
|
|
252
|
|
|
253 #TODO refactoring about min size of genome for preprocess
|
|
|
254 def selectContigs4givenSize(self,BSDB,limit=200000000):
|
|
|
255 if self._verbosity > 0:
|
|
|
256 print "Selecting contigs to reach %s pb "%limit
|
|
|
257 contigsHeadersAndLength=zip(BSDB.getHeaderList(),BSDB.getListOfSequencesLength())
|
|
|
258 size=0
|
|
|
259 size_small=0
|
|
|
260 size_big=500000000
|
|
|
261 lselectedContigs=[]
|
|
|
262
|
|
|
263 for seq in BSDB.db :
|
|
|
264 size+=seq.getLength()
|
|
|
265 if size<limit:
|
|
|
266 lselectedContigs.append(seq)
|
|
|
267 size_small=size
|
|
|
268 else :
|
|
|
269 size_big=size
|
|
|
270 break
|
|
|
271
|
|
|
272 if size_big-limit<limit-size_small :
|
|
|
273 lselectedContigs.append(seq)
|
|
|
274
|
|
|
275 if self._verbosity > 0:
|
|
|
276 print "%s contigs selected to reach %s pb (%s contigs initially) "%(len(lselectedContigs),limit,len(contigsHeadersAndLength))
|
|
|
277
|
|
|
278 selectedContigsBSDB=BioseqDB()
|
|
|
279 selectedContigsBSDB.setData(lselectedContigs)
|
|
|
280 return selectedContigsBSDB
|
|
|
281
|
|
|
282 def writeFastaInput(self,BSDB,outFileName=''):
|
|
|
283 if self._verbosity > 0:
|
|
|
284 print "Writing fasta file"
|
|
|
285
|
|
|
286 if not outFileName:
|
|
|
287 outFileName = self._projectName + ".fastaExtract"
|
|
|
288
|
|
|
289 BSDB.save(outFileName)
|
|
|
290 if self._verbosity > 0:
|
|
|
291 print '%d sequences saved.'%BSDB.getSize()
|
|
|
292
|
|
|
293 return outFileName
|
|
|
294
|
|
|
295 def correctHeader(self,BSDB):
|
|
|
296 if self._verbosity > 0:
|
|
|
297 print "Correcting fasta headers"
|
|
|
298 replacedSeqNb=0
|
|
|
299 for header in BSDB.getHeaderList() :
|
|
|
300 p = re.compile('[^a-zA-Z0-9_:\.\-]', re.IGNORECASE)
|
|
|
301 if p.search(header):
|
|
|
302 sub=list(set(p.findall(header)))
|
|
|
303 correctedHeader=header
|
|
|
304 for s in sub :
|
|
|
305 correctedHeader=correctedHeader.replace(s,'_')
|
|
|
306 if self._verbosity>2:
|
|
|
307 print "Correct Header : '%s' replaced by '%s'"%(header,correctedHeader)
|
|
|
308 BSDB.fetch(header).setHeader(correctedHeader)
|
|
|
309 replacedSeqNb+=1
|
|
|
310 if self._verbosity > 0:
|
|
|
311 print '%s sequence headers corrected'%replacedSeqNb
|
|
|
312 return BSDB
|
|
|
313
|
|
|
314
|
|
|
315 def _launchTEdenovo(self):
|
|
|
316 print "START time: %s" % time.strftime("%Y-%m-%d %H:%M:%S")
|
|
|
317 lCmds = []
|
|
|
318 lCmds.append( "TEdenovo.py -P %s -C %s -S 1 -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
319 lCmds.append( "TEdenovo.py -P %s -C %s -S 2 -s Blaster -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
320 lCmds.append( "TEdenovo.py -P %s -C %s -S 3 -s Blaster -c Grouper -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
321 lCmds.append( "TEdenovo.py -P %s -C %s -S 3 -s Blaster -c Recon -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
322 lCmds.append( "TEdenovo.py -P %s -C %s -S 3 -s Blaster -c Piler -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
323 lCmds.append( "TEdenovo.py -P %s -C %s -S 4 -s Blaster -c Grouper -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
324 lCmds.append( "TEdenovo.py -P %s -C %s -S 4 -s Blaster -c Recon -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
325 lCmds.append( "TEdenovo.py -P %s -C %s -S 4 -s Blaster -c Piler -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
326 lCmds.append( "TEdenovo.py -P %s -C %s -S 5 -s Blaster -c GrpRecPil -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
327 lCmds.append( "TEdenovo.py -P %s -C %s -S 6 -s Blaster -c GrpRecPil -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
328 lCmds.append( "TEdenovo.py -P %s -C %s -S 7 -s Blaster -c GrpRecPil -m Map -v %i" % (self._projectName, self._configFileName, self._verbosity) )
|
|
|
329
|
|
|
330 for cmd in lCmds:
|
|
|
331 returnValue = os.system(cmd)
|
|
|
332 if returnValue != 0:
|
|
|
333 print "ERROR: command '%s' returned %i" % (cmd, returnValue)
|
|
|
334 self._cleanTables()
|
|
|
335 sys.exit(1)
|
|
|
336
|
|
|
337 print "END time: %s" % time.strftime("%Y-%m-%d %H:%M:%S")
|
|
|
338 outFastaFile = glob.glob("%s_Blaster_GrpRecPil_Map_TEclassif_Filtered/*_denovoLibTEs_filtered.fa"%self._projectName)
|
|
|
339 shutil.copy(outFastaFile[0], self._outputFasta)
|
|
|
340 outStatsFile = glob.glob("%s_Blaster_GrpRecPil_Map_TEclassif_Filtered/*.classif_stats.txt"%self._projectName)
|
|
|
341 shutil.copy(outStatsFile[0], self._outputStats)
|
|
|
342 if self._classif:
|
|
|
343 outClassifFile = glob.glob("%s_Blaster_GrpRecPil_Map_TEclassif/classifConsensus/*_withoutRedundancy_negStrandReversed_WickerH.classif"%self._projectName)
|
|
|
344 shutil.copy(outClassifFile[0], self._outputClassif)
|
|
|
345 self._renameTE()
|
|
|
346
|
|
|
347 def _renameTE(self):
|
|
|
348 name=re.search(r'([^\/\\]*)-\d{8}-denovoLibTEs_filtered\.[fa|fasta|fsa|fas]',self._outputFasta).groups()[0]
|
|
|
349 os.system("sed -i 's|%s|%s|' %s" % (self._projectName,name, self._outputFasta))
|
|
|
350 if self._classif:
|
|
|
351 os.system("sed -i 's|%s|%s|' %s" % (self._projectName,name, self._outputClassif))
|
|
|
352
|
|
|
353 def preprocessFastaFile(self):
|
|
|
354 inFileHandler = open(self._fastaFileName, "r")
|
|
|
355 cumulLength = FastaUtils.dbCumLength(inFileHandler)
|
|
|
356 inFileHandler.close()
|
|
|
357 if cumulLength >= self._limitSeqSize:
|
|
|
358 print "Preprocess lauched"
|
|
|
359 allContigsBSDB=self.removeNstretches()
|
|
|
360 selectedContigsBSDB=self.selectContigs4givenSize(allContigsBSDB)
|
|
|
361 self.correctHeader(selectedContigsBSDB)
|
|
|
362 fastaFile=self.writeFastaInput(selectedContigsBSDB)
|
|
|
363 print "Preprocess finished"
|
|
|
364 else:
|
|
|
365 fastaFile=self._fastaFileName
|
|
|
366 print "No preprocess : the genome size %s lower than %s Mbp" % (cumulLength, self._limitSeqSize/1000000)
|
|
|
367 os.symlink(fastaFile,"%s/%s.fa" %(os.getcwd(),self._projectName)) #creer repertoire projet
|
|
|
368
|
|
|
369 def _launchListAndDropTables(self):
|
|
|
370 cmd = "ListAndDropTables.py"
|
|
|
371 cmd += " -C %s" % self._configFileName
|
|
|
372 cmd += " -d '%s'" % self._projectName
|
|
|
373 os.system(cmd)
|
|
|
374
|
|
|
375 def _cleanJobsTable(self):
|
|
|
376 db = DbFactory.createInstance( configFileName = self._configFileName )
|
|
|
377 sql_cmd="DELETE FROM jobs WHERE groupid like '%s%%';"%self._projectName
|
|
|
378 db.execute( sql_cmd )
|
|
|
379 db.close()
|
|
|
380
|
|
|
381 def _cleanTables(self):
|
|
|
382 self._launchListAndDropTables()
|
|
|
383 self. _cleanJobsTable()
|
|
|
384
|
|
|
385
|
|
|
386 def run(self):
|
|
|
387 os.mkdir(self._projectName)
|
|
|
388 os.chdir(self._projectName)
|
|
|
389 self._writeConfigFile()
|
|
|
390 self.preprocessFastaFile()
|
|
|
391 if self._nucl_bank != "" and self._nucl_bank != None:
|
|
|
392 os.symlink(self._nucl_bank,"%s/%s" %(os.getcwd(),os.path.basename(self._nucl_bank)))
|
|
|
393 if self._prot_bank != "" and self._prot_bank != None:
|
|
|
394 os.symlink(self._prot_bank,"%s/%s" %(os.getcwd(),os.path.basename(self._prot_bank)))
|
|
|
395 if self._HMM_profiles != "" and self._HMM_profiles != None:
|
|
|
396 os.symlink(self._HMM_profiles,"%s/%s" %(os.getcwd(),os.path.basename(self._HMM_profiles)))
|
|
|
397 if self._rdna_bank != "" and self._rdna_bank != None:
|
|
|
398 os.symlink(self._rdna_bank,"%s/%s" %(os.getcwd(),os.path.basename(self._rdna_bank)))
|
|
|
399
|
|
|
400 self._launchTEdenovo()
|
|
|
401 self._cleanTables()
|
|
|
402
|
|
|
403 if __name__ == '__main__':
|
|
|
404 iTEdenovo = TEdenovo_lite()
|
|
|
405 iTEdenovo.setAttributesFromCommandLine()
|
|
|
406 iTEdenovo.run()
|
