def dbGCperc(inFileName): """ deprecated """ file_db=open(inFileName) seq=Bioseq() numseq=0 sum_count=0 sum_nb=0 while 1: seq.read(file_db) if seq.sequence==None: break numseq=numseq+1 occ,nb=seq.occ_word(1) count=0 for i in occ.keys(): if i == "G" or i=="C": count+=occ[i] if nb!=0 : print 'sequence #',numseq,'=','[',seq.header[0:20],'...]',float(count)/nb sum_count+=count sum_nb+=nb print "Total:",float(sum_count)/sum_nb, sum_count file_db.close()
def dbWord(inFileName,wordsize):
"""
deprecated
"""
vec_len=[]
file_db=open(inFileName)
seq=Bioseq()
numseq=0
nb_word=0
statCount={}
while 1:
seq.read(file_db)
if seq.sequence==None:
break
numseq=numseq+1
print 'sequence #',numseq,'=',seq.getLength(),'[',seq.header[0:40],'...]'
occ,nb=seq.occ_word(wordsize)
nb_word=nb_word+nb
for i in occ.keys():
if i not in statCount.keys():
statCount[i]=occ[i]
else:
statCount[i]=statCount[i]+occ[i]
file_db.close()
vec_sort=[]
for i in statCount.keys():
vec_sort.append((-float(statCount[i])/nb_word,i))
vec_sort.sort()
for i in vec_sort:
print i[1],"=",-i[0]
def dbRelEntropy(inFileName,wordsize):
"""
deprecated
"""
file_db=open(inFileName)
seq=Bioseq()
refocc={}
sumlen=0
while 1:
seq.read(file_db)
if seq.sequence==None:
break
sumlen=sumlen+seq.getLength()-wordsize
occ=seq.occ_word(wordsize)
if(len(refocc)==0):
refocc=occ
else:
for w in occ.keys():
if refocc.has_key(w):
refocc[w]=refocc[w]+occ[w]
else:
refocc[w]=occ[w]
file_db.close()
reffreq={}
for w in refocc.keys():
reffreq[w]=float(refocc[w]+1)/sumlen
vec_len=[]
stat=Stat()
file_db=open(inFileName)
numseq=0
while 1:
seq.read(file_db)
if seq.sequence==None:
break
i=seq.rel_entropy(reffreq)
stat.add(i)
numseq=numseq+1
print 'sequence #',numseq,'=',seq.getLength(),'[',seq.header[0:40],'...] entropy',i
vec_len.append((i,numseq,seq.header))
file_db.close()
vec_len.sort()
for s in vec_len:
print 'H=',s[0],'=> #',s[1], s[2]
print stat.string()
return vec_len