def dbTraduit(inFileName,phase=0,complement='T',pep_filename=""): """ deprecated """ file_db=open(inFileName) if pep_filename=="": pep_filename=inFileName+'.pep' file_pep=open(pep_filename,'w') seq=Bioseq() seq_out=Bioseq() numseq=0 while 1: seq.read(file_db) if seq.sequence==None: break numseq=numseq+1 print 'sequence #',numseq,'=',seq.getLength(),\ '[',seq.header[0:40],'...]' if phase>=0 : if phase==1 or phase==0 : seq_out.sequence=seq.traduit(1) seq_out.header=seq.header+" (phase 1)" seq_out.write(file_pep) if phase==2 or phase==0 : seq_out.sequence=seq.traduit(2) seq_out.header=seq.header+" (phase 2)" seq_out.write(file_pep) if phase==3 or phase==0 : seq_out.sequence=seq.traduit(3) seq_out.header=seq.header+" (phase 3)" seq_out.write(file_pep) if complement=='T' or phase<0 : seq.sequence=seq.complement() if phase==-1 or phase==0 : seq_out.sequence=seq.traduit(1) seq_out.header=seq.header+" (phase -1)" seq_out.write(file_pep) if phase==-2 or phase==0 : seq_out.sequence=seq.traduit(2) seq_out.header=seq.header+" (phase -2)" seq_out.write(file_pep) if phase==-3 or phase==0 : seq_out.sequence=seq.traduit(3) seq_out.header=seq.header+" (phase -3)" seq_out.write(file_pep) file_db.close() file_pep.close()
def sortSequencesByIncreasingLength( inFile, outFile, verbose=0 ):
"""
Save sequences in 'inFile' into 'outFile' sorted by their length in increasing order.
"""
if verbose > 0:
print "sort sequences by increasing length"
sys.stdout.flush()
if not os.path.exists( inFile ):
print "ERROR: file '%s' doesn't exist" % ( inFile )
sys.exit(1)
# read each seq one by one
# save them in distinct temporary files
# with their length in the name
inFileHandler = open( inFile, "r" )
bs = Bioseq()
countSeq = 0
while True:
bs.read( inFileHandler )
if bs.header == None:
break
countSeq += 1
tmpFile = "%ibp_%inb" % ( bs.getLength(), countSeq )
bs.save( 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( outFile ):
os.remove( outFile )
lFiles = glob.glob( "*bp_*nb" )
lFiles.sort( key=lambda s:int(s.split("bp_")[0]) )
for fileName in lFiles:
cmd = "cat %s >> %s" % ( fileName, outFile )
returnValue = os.system( cmd )
if returnValue != 0:
print "ERROR while concatenating '%s' with '%s'" % ( fileName, outFile )
sys.exit(1)
os.remove( fileName )
return 0
def dbComplement(inFileName,comp_filename=""): """ deprecated """ file_db=open(inFileName) if comp_filename=="": comp_filename=inFileName+'.comp' file_comp=open(comp_filename,'w') seq=Bioseq() numseq=0 while 1: seq.read(file_db) if seq.sequence==None: break numseq=numseq+1 print 'sequence #',numseq,'=',seq.getLength(),'[',seq.header[0:40],'...]' seq.sequence=seq.complement() seq.header=seq.header+" (complement!)" seq.write(file_comp) file_db.close() file_comp.close()
def dbConsensus(filename,consensus_filename,max_set_size=20,max_len=20000,min_len=50,min_base_nb=1):
"""
deprecated
"""
os.system("orienter "+filename)
tmp_consensus_filename=filename+".oriented.consensus.tmp"
size_db=dbSize(filename+".oriented")
file_in=open(filename+".oriented")
file_out=open(consensus_filename,'w')
seq=Bioseq()
if size_db==1:
seq.read(file_in)
seq.header="not a consensus"
seq.write(file_out)
file_out.close()
file_in.close()
os.system("cp "+filename+".oriented"+
" "+filename+
".malign.fa")
os.system("cp "+filename+".oriented"+
" "+filename+
".malign.fa.cons")
sys.exit(1)
seq_in_set=0
nb_consensus=0
count_set=0
set_size=size_db
while set_size>max_set_size:
set_size=set_size/2
tmp_file_out=open(tmp_consensus_filename,'w')
last_seq=0
while 1:
#read subset of sequence
seq.read(file_in)
if seq.sequence!=None:
if seq.getLength() < max_len and seq.getLength() > min_len:
seq.write(tmp_file_out)
seq_in_set=seq_in_set+1
else:
if seq.getLength() > max_len:
print seq.header+" too long!!"
if not seq.header.find(" too long, not aligned"):
seq.header=seq.header+" too long, not aligned"
seq.write(file_out)
if seq.getLength() < min_len:
print seq.header+" too short!!"
else:
last_seq=1
if seq_in_set==0:
return count_set
# aligne subset
if seq_in_set==set_size or last_seq:
count_set=count_set+1
print "aligning the set #",count_set," of ",seq_in_set," sequences"
tmp_file_out.close()
if seq_in_set>1:
os.system("nice malign "+tmp_consensus_filename
+" 20 -8 16 4 > "
+tmp_consensus_filename+".malign"
+str(count_set)+".fa")
os.system("nice consensusFastaAli.py -n "
+str(min_base_nb)+" "
+tmp_consensus_filename
+".malign"+str(count_set)+".fa ")
os.system("cp "+tmp_consensus_filename+
".malign"+str(count_set)+".fa "
+filename+
".malign"+str(count_set)+".fa")
else:
os.system("cp "+tmp_consensus_filename+
" "+filename+
".malign"+str(count_set)+".fa")
os.system("cp "+tmp_consensus_filename+
" "+tmp_consensus_filename+
".malign"+str(count_set)+".fa.cons")
os.system("cat "+tmp_consensus_filename+
".malign"+str(count_set)+\
".fa.cons >> "+consensus_filename)
seq_in_set=0
tmp_file_out=open(tmp_consensus_filename,'w')
if set_size==size_db or last_seq: break
tmp_file_out.close()
file_out.close()
file_in.close()
os.system("rm "+tmp_consensus_filename+"* "+filename+".oriented" )
return count_set
