def dbORF( inFileName, orfMaxNb = 0, orfMinLength = 0, outFileName = "", verbose=0 ):
if outFileName == "":
outFileName = inFileName + ".orf.map"
outFile = open( outFileName, "w" )
bioseq = Bioseq()
bioseqNb = 0
inFile = open( inFileName )
while True:
bioseq.read( inFile )
if bioseq.sequence == None:
break
bioseq.upCase()
bioseqNb += 1
if verbose > 0:
print 'sequence num',bioseqNb,'=',bioseq.getLength(),'[',bioseq.header[0:40],'...]'
orf = bioseq.findORF()
bestOrf = []
for i in orf.keys():
orfLen = len(orf[i])
for j in xrange(1, orfLen):
start = orf[i][j-1] + 4
end = orf[i][j] + 3
if end - start >= orfMinLength:
bestOrf.append( ( end-start, i+1, start, end ) )
bioseq.complement()
orf = bioseq.findORF()
seqLen = bioseq.getLength()
for i in orf.keys():
orfLen = len(orf[i])
for j in xrange(1, orfLen):
start = seqLen - orf[i][j-1] - 3
end = seqLen - orf[i][j] - 2
if start - end >= orfMinLength:
bestOrf.append( ( start-end, (i+1)*-1, start, end ) )
bestOrf.sort()
bestOrf.reverse()
bestOrfNb = len(bestOrf)
if orfMaxNb > bestOrfNb or orfMaxNb == 0 :
orfMaxNb = bestOrfNb
for i in xrange(0, orfMaxNb):
if verbose > 0:
print bestOrf[i]
outFile.write("%s\t%s\t%d\t%d\n"%("ORF|"+str(bestOrf[i][1])+\
"|"+str(bestOrf[i][0]),bioseq.header,
bestOrf[i][2],bestOrf[i][3]))
inFile.close()
outFile.close()
return 0
def dbLengthFilter( len_min, inFileName, verbose=0 ):
file_db = open( inFileName, "r" )
file_dbInf = open( inFileName+".Inf"+str(len_min), "w" )
file_dbSup = open( inFileName+".Sup"+str(len_min), "w" )
seq = Bioseq()
numseq = 0
nbsave = 0
while True:
seq.read( file_db )
if seq.sequence == None:
break
l = seq.getLength()
numseq = numseq + 1
if l >= len_min:
seq.write( file_dbSup )
if verbose > 0:
print 'sequence #',numseq,'=',l,'[',seq.header[0:40],'...] Sup !!'
nbsave=nbsave+1
else:
seq.write( file_dbInf )
if verbose > 0:
print 'sequence #',numseq,'=',l,'[',seq.header[0:40],'...] Inf !!'
nbsave=nbsave+1
file_db.close()
file_dbInf.close()
file_dbSup.close()
if verbose > 0:
print nbsave,'saved sequences in ',inFileName+".Inf"+str(len_min)," and ", inFileName+".Sup"+str(len_min)
def createSeqTable( self, tableName, fileName = "" ):
sqlCmd = "CREATE TABLE %s (accession varchar(255), sequence longtext, description varchar(255), length int unsigned )" % (tableName)
self.execute( sqlCmd )
self.createSeqIndex( tableName )
self.updateInfoTable( tableName, fileName )
if fileName != "":
inFile = open( fileName )
tmpFileName = fileName.split("/")[-1] + ".tmp" + str(os.getpid())
tmpFile = open(tmpFileName, "w")
bioseq = Bioseq()
seqNb = 0
while True:
bioseq.read( inFile )
if bioseq.sequence == None:
break
seqLen = bioseq.getLength()
tmpFile.write("%s\t%s\t%s\t%d\n" % (bioseq.header.split()[0], \
bioseq.sequence, bioseq.header, seqLen))
seqNb += 1
inFile.close()
tmpFile.close()
sqlCmd = "LOAD DATA LOCAL INFILE '%s' IGNORE INTO TABLE %s FIELDS ESCAPED BY ''" % \
(tmpFileName, tableName)
self.execute( sqlCmd )
os.remove( tmpFileName )
def sortSequencesByIncreasingLength(inFileName, outFileName, verbose=0):
if verbose > 0:
print "sort sequences by increasing length"
sys.stdout.flush()
if not os.path.exists( inFileName ):
print "ERROR: file '%s' doesn't exist" % ( inFileName )
sys.exit(1)
# read each seq one by one
# save them in distinct temporary files
# with their length in the name
inFileHandler = open( inFileName, "r" )
bs = Bioseq()
countSeq = 0
while True:
bs.read( inFileHandler )
if bs.header == None:
break
countSeq += 1
tmpFile = "%ibp_%inb" % ( bs.getLength(), countSeq )
bs.appendBioseqInFile( tmpFile )
if verbose > 1:
print "%s (%i bp) saved in '%s'" % ( bs.header, bs.getLength(), tmpFile )
bs.header = ""
bs.sequence = ""
inFileHandler.close()
# sort temporary file names
# concatenate them into the output file
if os.path.exists( outFileName ):
os.remove( outFileName )
lFiles = glob.glob( "*bp_*nb" )
lFiles.sort( key=lambda s:int(s.split("bp_")[0]) )
for fileName in lFiles:
cmd = "cat %s >> %s" % ( fileName, outFileName )
returnValue = os.system( cmd )
if returnValue != 0:
print "ERROR while concatenating '%s' with '%s'" % ( fileName, outFileName )
sys.exit(1)
os.remove( fileName )
return 0
def getLengthPerSeqFromFile( inFile ):
dHeader2Length = {}
inFileHandler = open( inFile, "r" )
while True:
iBs = Bioseq()
iBs.read( inFileHandler )
if iBs.sequence == None:
break
dHeader2Length[ iBs.header ] = iBs.getLength()
inFileHandler.close()
return dHeader2Length
def filterClassifiedConsensus( self ):
inFile = open( self._inFaFile, "r" )
outFile = open( self._outFaFile, "w" )
bs = Bioseq()
nbInSeq = 0
nbRmv = 0
if self._classifFile != "":
dHeader2Classif = self.getClassifPerHeaderOfUnclassifiedConsensus()
while True:
bs.read( inFile )
if bs.header == None:
break
nbInSeq += 1
if self._verbose > 1:
print bs.header
if self._filterSSRs and "SSR" in bs.header and ( self._maxLengthToFilterSSRs == 0 or bs.getLength() <= self._maxLengthToFilterSSRs ):
nbRmv += 1
if self._verbose > 1: print "filtered SSR !"
elif self._filterHostGenes and "HostGene" in bs.header:
nbRmv += 1
if self._verbose > 1: print "filtered HostGene !"
elif self._filterConfused and "confused" in bs.header and "confusedness=no" not in bs.header:
nbRmv += 1
if self._verbose > 1: print "filtered confused !"
elif self._filterNoCat != "0" and "NoCat" in bs.header:
keep = False
if "2" in self._filterNoCat:
algoMSA = ""
for i in ["Map","MAP","Malign","Mafft","Prank","Clustalw","Muscle","Tcoffee"]:
if i in bs.header:
algoMSA = i
nbAlignSeq = int( bs.header.split(algoMSA+"_")[1].split("|")[0] )
if nbAlignSeq > self._nbAlignSeqNoCat:
keep = True
if "3" in self._filterNoCat:
for header in dHeader2Classif.keys():
if header in bs.header:
if "no structural features" not in dHeader2Classif[header][6]:
keep = True
if keep:
bs.write( outFile )
else:
nbRmv += 1
if self._verbose > 1: print "filtered NoCat !"
elif self._filterIncomplete and "completeness=incomp" in bs.header:
nbRmv += 1
if self._verbose > 1: print "filtered incomplete !"
else:
bs.write( outFile )
inFile.close()
outFile.close()
if self._verbose > 0:
print "nb of input seq: %i" % ( nbInSeq )
print "nb of filtered seq: %i" % ( nbRmv )
sys.stdout.flush()
