class TranslateInAllFramesAndReplaceStopByX( object ):
def __init__(self):
self.fileUtils = FileUtils()
self.bioseq = pyRepet.seq.Bioseq.Bioseq()
self._inputFile = ""
self._outputFile = ""
self._bioseqUtils = pyRepet.seq.BioseqUtils.BioseqUtils
def setInputFile(self, input):
self._inputFile = input
def setOutputFile(self, output):
self._outputFile = output
def run(self):
"""
read a fasta file with nucleotide sequences and translate all sequences in all frames, write the result in a file
"""
if not self.fileUtils.isRessourceExists(self._inputFile):
print "Warning your input file " + self._inputFile + " does not exist!\n"
return
bioseqList = self._bioseqUtils.extractBioseqListFromFastaFile(self._inputFile)
# translate in All frames
bioseqListInAllFrames = self._bioseqUtils.translateBioseqListInAllFrames(bioseqList)
#replace Stops by X
bioseqListTranslatedAndStopsReplace = self._bioseqUtils.replaceStopCodonsByXInBioseqList( bioseqListInAllFrames )
# write in a file
self._bioseqUtils.writeBioseqListIntoFastaFile(bioseqListTranslatedAndStopsReplace, self._outputFile)
def __init__(self):
self.fileUtils = FileUtils()
self.bioseq = pyRepet.seq.Bioseq.Bioseq()
self._inputFile = ""
self._outputFile = ""
self._bioseqUtils = pyRepet.seq.BioseqUtils.BioseqUtils
class programLauncher( object ):
#--------------------------------------------------------------------------
def __init__( self, inFileName="", outFileName = "" ):
self.inFileName = inFileName
self._OutputFile = outFileName
self.fileUtils = FileUtils()
#--------------------------------------------------------------------------
def reset( self, inFileName ):
self.inFileName = inFileName
#--------------------------------------------------------------------------
def setOutputFileName( self, outFileName ):
self._OutputFile = outFileName
#--------------------------------------------------------------------------
def _checkFileExistsAndNotEmpty(self, fileName):
if self.fileUtils.isRessourceExists(fileName) and not self.fileUtils.isFileEmpty(fileName):
return 1
return 0
#--------------------------------------------------------------------------
def launch( self, prg, cmd, verbose=0 ):
# slowly switch from yes/no to 0/1/2/...
if verbose == "yes":
verbose = 1
if verbose == "no":
verbose = 0
if verbose > 0:
print "beginning of %s" % ( prg ); sys.stdout.flush()
log = os.system( cmd )
if log == 0:
if verbose > 0:
print "%s finished successfully" % ( prg ); sys.stdout.flush()
return 0
else:
print "*** Error: %s returned %i" % ( prg, log )
print "time: %s" % ( time.strftime("%Y-%m-%d %H:%M:%S") )
sys.exit(1)
#--------------------------------------------------------------------------
def launchBlaster( self, subjectBankName="", allByAll="no", blastVersion="NCBI", blastAlgo="blastn", blastOpt="", cutLgth="50000", cutOver="100", cutWord="11", cutExt="_cut", sensitiv="0", evalFilter="1e-10", idFilter="0", lgthFilter="20", outPrefix="", reRunAll="no", prepareOnly="no", run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/blaster"
cmd = prg
cmd += " -q " + self.inFileName
if subjectBankName != "":
cmd += " -s " + subjectBankName
if allByAll == "yes":
cmd += " -a"
if blastVersion != "NCBI":
cmd += " -W"
if blastAlgo != "blastn":
cmd += " -n " + blastAlgo
if blastOpt != "":
cmd += " -p " + blastOpt
if cutLgth != "50000":
cmd += " -l " + cutLgth
if cutOver != "100":
cmd += " -o " + cutOver
if cutWord != "11":
cmd += " -w " + str(cutWord)
if cutExt != "_cut":
cmd += " -e " + cutExt
if sensitiv != "0":
cmd += " -S " + sensitiv
if evalFilter != "1e-10":
cmd += " -E " + evalFilter
if idFilter != "0":
cmd += " -I " + idFilter
if lgthFilter != "20":
cmd += " -L " + str(lgthFilter)
if outPrefix != "":
cmd += " -B " + outPrefix
if reRunAll != "no":
cmd += " -r"
if prepareOnly != "no":
cmd += " -P"
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchGrouper( self, matchFileName, subjectBankName="", joinMatch="no", idTolerance="2", gapPenalty="0.05", distPenalty="0.2", authOver="20", evalFilter="1e-10", idFilter="0", lgthFilter="20", outPrefix="", covConnectGrp="100", rmvGrp="no", covGrp="0.95", grpSizeFilter="1", run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/grouper"
cmd = prg
cmd += " -m " + matchFileName
cmd += " -q " + self.inFileName
if subjectBankName != "":
cmd += " -s " + subjectBankName
if joinMatch != "no":
cmd += " -j"
if idTolerance != "2":
cmd += " -i " + idTolerance
if gapPenalty != "0.05":
cmd += " -g " + gapPenalty
if distPenalty != "0.2":
cmd += " -d " + distPenalty
if authOver != "20":
cmd += " -c " + authOver
if evalFilter != "1e-10":
cmd += " -E " + evalFilter
if idFilter != "0":
cmd += " -I " + idFilter
if lgthFilter != "20":
cmd += " -L " + lgthFilter
if outPrefix != "":
cmd += " -B " + outPrefix
if covConnectGrp != "100":
cmd += " -G " + covConnectGrp
if rmvGrp != "no":
cmd += " -X " + rmvGrp
if covGrp != "0.95":
cmd += " -C " + covGrp
if grpSizeFilter != "1":
cmd += " -Z " + grpSizeFilter
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMatcher( self, queryBankName="", subjectBankName="", joinMatch="no", idTolerance="2", gapPenalty="0.05", distPenalty="0.2", authOver="20", evalFilter="1e-10", idFilter="0", lgthFilter="20", outPrefix="", keepAllConflictSbj=False, run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/matcher"
cmd = prg
cmd += " -m " + self.inFileName
if queryBankName != "":
cmd += " -q " + queryBankName
if subjectBankName != "":
cmd += " -s " + subjectBankName
if joinMatch != "no":
cmd += " -j"
if idTolerance != "2":
cmd += " -i " + idTolerance
if gapPenalty != "0.05":
cmd += " -g " + gapPenalty
if distPenalty != "0.2":
cmd += " -d " + distPenalty
if authOver != "20":
cmd += " -c " + authOver
if evalFilter != "1e-10":
cmd += " -E " + evalFilter
if idFilter != "0":
cmd += " -I " + idFilter
if lgthFilter != "20":
cmd += " -L " + lgthFilter
if outPrefix != "":
cmd += " -B " + outPrefix
if keepAllConflictSbj == True:
cmd += " -a"
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchCutterDB( self, length="50000", overlap="100", wordN="11", run="yes", verbose=0 ):
# slowly switch from yes/no to 0/1/2/...
if verbose == "yes":
verbose = 1
if verbose == "no":
verbose = 0
prg = os.environ["REPET_PATH"] + "/bin/cutterDB"
cmd = prg
cmd += " -l " + length
cmd += " -o " + overlap
cmd += " -w " + wordN
cmd += " " + self.inFileName
if verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose-1 )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMap2db( self, faFileName, merge=False, flankSize="0", run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/map2db"
cmd = prg
if merge == True:
cmd += " -m"
cmd += " -s %s" % ( flankSize )
cmd += " %s" % ( self.inFileName )
cmd += " %s" % ( faFileName )
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchTRsearch( self, run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/TRsearch"
cmd = prg
cmd += " " + self.inFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchPolyAtail( self, run="yes", verbose="no" ):
prg = os.environ["REPET_PATH"] + "/bin/polyAtail"
cmd = prg
cmd += " " + self.inFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchPals( self, subjectBankName="", selfAlign="yes", out="stdout", lgthFilter="400", idFilter="94", run="yes", verbose="no" ):
prg = "pals"
cmd = prg
if subjectBankName == "" and selfAlign == "yes":
cmd += " -self " + self.inFileName
elif subjectBankName != "" and selfAlign != "yes":
cmd += " -target " + subjectBankName
cmd += " -query " + self.inFileName
if out != "stdout":
cmd += " -out " + out
if lgthFilter != "400":
cmd += " -length " + lgthFilter
if idFilter != "94":
cmd += " -pctid " + idFilter
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMap( self, outFileName, gapSize="50", mismatch="-8", gapOpen="16", gapExtend="4", run="yes", verbose="no" ):
print "DEPRECATED"
prg = os.environ["REPET_PATH"] + "/bin/rpt_map"
cmd = prg
cmd += " " + self.inFileName
cmd += " " + gapSize
cmd += " " + mismatch
cmd += " " + gapOpen
cmd += " " + gapExtend
cmd += " > " + outFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchRefalign( self, outFileName, gapSize="10", match="10", mismatch="-8", gapOpen="16", gapExtend="4", refseqName="", run="yes", verbose="no" ):
refFileName=self.inFileName + ".ref"
cpyFileName=self.inFileName + ".cpy"
file_db=open(self.inFileName)
file_ref=open(refFileName,"w")
file_cpy=open(cpyFileName,"w")
numseq=0
while 1:
seq=Bioseq()
seq.read(file_db)
if seq.sequence==None:
break
numseq+=1
if numseq==1:
seq.write(file_ref)
else:
seq.write(file_cpy)
file_db.close()
file_ref.close()
file_cpy.close()
if numseq > 1:
prg = os.environ["REPET_PATH"] + "/bin/refalign"
cmd = prg
cmd += " " + refFileName
cmd += " " + cpyFileName
cmd += " -m " + match
cmd += " -l " + gapSize
cmd += " -d " + mismatch
cmd += " -g " + gapOpen
cmd += " -e " + gapExtend
cmd += " ; "
cmd += os.environ["REPET_PATH"] + "/bin/refalign2fasta.py"
cmd += " -i " + cpyFileName + ".aligner"
if refseqName != "":
cmd += " -r %s" % ( refseqName )
cmd += " -g d"
cmd += " -o " + outFileName
if verbose == "yes":
cmd += " -v 1"
cmd += " ; "
cmd += "rm -f "+refFileName + " " + cpyFileName + " " + cpyFileName + ".aligner " + cpyFileName + ".oriented " + cpyFileName + ".refalign.stat"
else:
prg = cmd = "echo empty"
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMafft( self, outFileName, run="yes", verbose=0 ):
print "DEPRECATED"
prg = "mafft"
cmd = prg
cmd += " --auto"
if verbose == "no" or verbose == 0:
cmd += " --quiet"
cmd += " " + self.inFileName
cmd += " > " + outFileName
if verbose == "yes" or verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMuscle( self, outFileName, run="yes", verbose="no" ):
prg = "muscle"
cmd = prg
cmd += " -in " + self.inFileName
cmd += " -out " + outFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchTcoffee( self, outFileName, param, run="yes", verbose=0 ):
prg = "t_coffee"
cmd = prg
if self.inFileName != "":
cmd += " -infile %s" % ( self.inFileName )
cmd += " -outfile %s" % ( outFileName )
cmd += " %s" % ( param )
if verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchPrank( self, outFileName, param, run="yes", verbose=0 ):
prg = "prank"
cmd = prg
cmd += " -d=%s" % ( self.inFileName )
cmd += " -o=%s" % ( outFileName )
cmd += " %s" % ( param )
if verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchClustalw( self, outFileName, run="yes", verbose="no" ):
prg = "clustalw"
cmd = prg
cmd += " -infile=" + self.inFileName
cmd += " -outfile=" + outFileName
cmd += " -output=fasta"
cmd += " -type=dna"
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchRepeatMasker( self ):
return 0
#--------------------------------------------------------------------------
def launchCensor( self ):
return 0
#--------------------------------------------------------------------------
def launchPhyML( self, dataType="0", seqFormat="i", nbDataSets="1", nbBootDataSets="0", substModel="HKY", ratioTsTv="4.0", propInvSites="e", nbCat="1", gammaParam="1.0", startTree="BIONJ", optTopology="y", optBranchRate="y", run="yes", verbose=0 ):
if verbose == "yes":
verbose = 1
if verbose == "no":
verbose = 0
prg = "phyml"
cmd = prg
cmd += " " + self.inFileName
cmd += " " + dataType
cmd += " " + seqFormat
cmd += " " + nbDataSets
cmd += " " + nbBootDataSets
cmd += " " + substModel
cmd += " " + ratioTsTv
cmd += " " + propInvSites
cmd += " " + nbCat
cmd += " " + gammaParam
cmd += " " + startTree
cmd += " " + optTopology
cmd += " " + optBranchRate
if verbose == 0:
cmd += " > /dev/null"
if verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchSreformat( self, outFormat, outFileName, run="yes", verbose=0 ):
if verbose == "yes":
verbose = 1
if verbose == "no":
verbose = 0
prg = "sreformat"
cmd = prg
cmd += " " + outFormat
cmd += " " + self.inFileName
cmd += " > " + outFileName
if verbose > 0:
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchTRF( self, match="2", mismatch="3", delta="5", pm="80", pi="10", minscore="20", maxperiod="15", html="no", dat="yes", run="yes", verbose="no" ):
prg = "trf"
cmd = prg
cmd += " " + self.inFileName
cmd += " " + match
cmd += " " + mismatch
cmd += " " + delta
cmd += " " + pm
cmd += " " + pi
cmd += " " + minscore
cmd += " " + maxperiod
if html == "no":
cmd += " -h"
if dat == "yes":
cmd += " -d"
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchMreps( self, outFileName, res="3", exp="3.0", maxsize="50", run="yes", verbose="no" ):
prg = "mreps"
cmd = prg
cmd += " -res " + res
cmd += " -exp " + exp
cmd += " -maxsize " + maxsize
cmd += " -xmloutput " + outFileName
cmd += " -fasta " + self.inFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchBlastclust( self, nbCPU="1", thresSimilarity="1.75", thresLengthCov="0.9", thresOnPair="T", outClustList="", outHitList="", prot="T", cfgFileName="", run="yes", verbose="no" ):
prg = "blastclust"
cmd = prg
cmd += " -i " + self.inFileName
if nbCPU != "1":
cmd += " -a " + nbCPU
if thresSimilarity != "1.75":
cmd += " -S " + thresSimilarity
if thresLengthCov != "0.9":
cmd += " -L " + thresLengthCov
if thresOnPair != "F":
cmd += " -b " + thresOnPair
if outClustList != "":
cmd += " -o " + outClustList
if outHitList != "":
cmd += " -s " + outHitList
if prot != "T":
cmd += " -p " + prot
if cfgFileName != "":
cmd += " -c " + cfgFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchShuffle( self, outFileName="", run="yes", verbose="no" ):
if CheckerUtils.isExecutableInUserPath("esl-shuffle"):
prg = "esl-shuffle"
else : prg = "shuffle"
cmd = prg
cmd += " -d " + self.inFileName
if outFileName != "":
cmd += " > " + outFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchDrawgram( self, outFileName="", run="yes", verbose="no" ):
prg = "drawgram"
cmd = prg
cmd += " <<EOF\n"
cmd += "%s\n" % ( self.inFileName )
cmd += "V\nN\nY\nEOF\n"
cmd += "mv plotfile %s" % ( outFileName )
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchSeqboot( self, nbReplicates="100", oddSeed="13579", outFileName="outfile", verbose=0 ):
"""
Launch 'seqboot' from the PHYLIP package.
"""
if os.path.exists( "outfile" ):
os.remove( "outfile" )
prg = "seqboot"
cmd = "echo '%s\nR\n%s\nI\nY\n%s' > file_options.txt\n" % ( self.inFileName, nbReplicates, oddSeed )
cmd += "cat file_options.txt | seqboot"
if verbose <= 0:
cmd += " > /dev/null"
cmd += "\n"
cmd += "rm file_options.txt\n"
if outFileName != "outfile":
cmd += "mv outfile %s\n" % ( outFileName )
return self.launch( prg, cmd, verbose )
#--------------------------------------------------------------------------
def launchHmmpfam( self, prg_path = "", evalFilter="10", inputFormat="FASTA", profilDatabank="", run="yes", verbose="no" ):
cmd = "hmmpfam"
if inputFormat != "":
cmd += " --informat " + inputFormat
if evalFilter != "":
cmd += " -E " + evalFilter
if profilDatabank != "":
cmd += " " + profilDatabank
cmd += " " + self.inFileName + " > " + self._OutputFile
if not self._checkFileExistsAndNotEmpty( self.inFileName ):
print "Warning : there is no input file : " + self.inFileName + "\n"
return 0
if self._OutputFile == "":
print "Warning : You must specify an outputFile name\n"
return 0
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg_path, cmd, verbose )
elif run == "no":
return cmd
#--------------------------------------------------------------------------
def launchPilerTA( self, outFileName, motifFileName, pyramidFileName, minhitcount="2", maxmargin="0.05", minratio="0.5", run="yes", verbose="no" ):
prg = "piler"
cmd = prg
cmd += " -tan " + self.inFileName
cmd += " -out " + outFileName
cmd += " -motif " + motifFileName
cmd += " -pyramid " + pyramidFileName
if verbose == "yes":
print "launch: %s" % ( cmd ); sys.stdout.flush()
if run == "yes":
return self.launch( prg, cmd, verbose )
elif run == "no":
return cmd
def __init__( self, inFileName="", outFileName = "" ):
self.inFileName = inFileName
self._OutputFile = outFileName
self.fileUtils = FileUtils()
def _concatPathFile(self, bank):
FileUtils.catFilesUsingPattern( "../batch_*.fa_BLRn_%s.align.clean_match.path" % ( bank ),
"%s_BLRn_%s.align.clean_match.path.tmp" % ( self._project, bank ) )