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Sequence Extract.py
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Sequence Extract.py
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def rc(seq):
'''
This function recieve DNA sequence and return sequence reverse complementary
'''
f=[]
for base in seq:
if base=="A":
f.append('T')
elif base=="T":
f.append('A')
elif base=="C":
f.append('G')
elif base=="G":
f.append('C')
f.reverse()
r=''.join(f)
return(r)
def gene_extract(fasta_file,Genbank_file):
'''
This function determine the start and end of each gene according to GenBank annotation and extract each gene in an indvedual fasta file
'''
t=open(fasta_file,'r')
r=open(Genbank_file,'r')
z=list(r)
k=list(t)
del k[0]
e=[]
for base in k:
mm=base.replace('\n','')
e.append(mm)
j=''.join(e)
c=0
x=[]
while c<=len(z)-1:
if 'gene ' in z[c]:
rr=z[c]+z[c+1]
x.append(rr)
c=c+1
else:
c=c+1
v=[]
b=[]
for base in x:
rr=base.split(' ')
b.append(rr[0])
v.append(rr[1])
m=[]
for base in v:
bhm=base.replace('"','')
bh=bhm.replace('\n','')
m.append(bh)
d=[]
for base in m:
bhm=base.replace('/gene=','')
bh=bhm.replace(' ','')
bhm=bh.replace('/','')
d.append(bhm)
i=[]
for base in b:
bhm=base.replace('complement','')
bh=bhm.replace('\n','')
bhm=bh.replace(' ','')
bh=bhm.replace('gene','')
bhm=bh.replace('join','')
bh=bhm.replace('(','')
bhm=bh.replace(')','')
i.append(bhm)
aw,u,g,ch=[],[],[],0
for base in i:
if ','in base:
ii=base.split(',')
u.append(ii[0])
u.append(ii[1])
g.append(d[ch])
g.append(d[ch]+'(1)')
ch=ch+1
else:
u.append(base)
g.append(d[ch])
ch=ch+1
vb,cc,hh,zz,hn=[],[],[],[],1
for base in u:
bn=base.split('..')
bb=int(bn[0])-1
qq=int(bn[1])-1
xc=(qq-bb)+1
hh.append(xc)
while bb<=qq:
vb.append(j[bb])
bb=bb+1
hn=hn+1
if hn==78:
vb.append('\n ')
hn=1
if bb==qq:
sc=''.join(vb)
we=len(sc)
zz.append(we)
vb=[]
cc.append(sc)
hn=1
uu=0
while uu<=len(cc)-1:
op=open(g[uu]+'.fas','w')
op.writelines('>'+str(hh[uu])+g[uu]+' macha\n')
op.writelines(cc[uu])
uu=uu+1
op.close()
return "Number of return Genes= "+ str(uu-1)
def intron_extract(fasta_file,Genbank_file):
'''
This function determine the start and end of each gene according to GenBank annotation and extract the whole entergenic regions in a single fasta file
'''
t=open(fasta_file,'r')
r=open(Genbank_file,'r')
z=list(r)
k=list(t)
del k[0]
e=[]
for base in k:
mm=base.replace('\n','')
e.append(mm)
j=''.join(e)
c=0
x=[]
while c<=len(z)-1:
if 'gene ' in z[c]:
rr=z[c]+z[c+1]
x.append(rr)
c=c+1
else:
c=c+1
v=[]
b=[]
for base in x:
rr=base.split(' ')
b.append(rr[0])
v.append(rr[1])
m=[]
for base in v:
bhm=base.replace('"','')
bh=bhm.replace('\n','')
m.append(bh)
d=[]
for base in m:
bhm=base.replace('/gene=','')
bh=bhm.replace(' ','')
bhm=bh.replace('/','')
d.append(bhm)
i=[]
for base in b:
bhm=base.replace('complement','')
bh=bhm.replace('\n','')
bhm=bh.replace(' ','')
bh=bhm.replace('gene','')
bhm=bh.replace('join','')
bh=bhm.replace('(','')
bhm=bh.replace(')','')
i.append(bhm)
aw,u,g,ch=[],[],[],0
for base in i:
if ','in base:
ii=base.split(',')
u.append(ii[0])
u.append(ii[1])
g.append(d[ch])
g.append(d[ch]+'(1)')
ch=ch+1
else:
u.append(base)
g.append(d[ch])
ch=ch+1
vb,cc,hh,zz,hn=[],[],[],[],1
for base in u:
bn=base.split('..')
bb=int(bn[0])-1
qq=int(bn[1])-1
xc=(qq-bb)+1
hh.append(xc)
while bb<=qq:
vb.append(j[bb])
bb=bb+1
hn=hn+1
if hn==78:
vb.append('\n ')
hn=1
if bb==qq:
sc=''.join(vb)
we=len(sc)
zz.append(we)
vb=[]
cc.append(sc)
hn=1
qqq=[]
for base in cc:
mer=base.replace('\n','')
sem=mer.replace(' ','')
qqq.append(sem)
aa=1
aaa=[]
ddd=[]
for base in qqq:
while aa<=len(base)-2:
aaa.append(base[aa])
aa=aa+1
cccc=''.join(aaa)
aa=1
aaa=[]
ddd.append(cccc)
rrr=[j]
for base in ddd:
if base in j:
vvv=rrr[0].replace(base,'NNNNN')
rrr.append(vvv)
del rrr[0]
else:
print('not found')
doc=rrr[0]
op=open('intron.fasta','w')
op.write(doc)
op.close()
return op
def primer_pick_up(Forward_primer,Reverse_primer, numer_of_fasta_files):
'''
This function return the sequence between forward and reverse primers
'''
a=Forward_primer
b=Reverse_primer
c=rc(Reverse_primer)
d=rc(Forward_primer)
pm=1
while pm<=numer_of_fasta_files:
op=open(str(pm)+'.fas','r')
z=list(op)
xx=z[0].replace('\n','')
doc=z[0]
del z[0]
r=''.join(z)
x=r.replace('\n','')
e=x.replace(a,'-'+a)
f=e.replace(b,b+'-')
g=f.replace(c,'-'+c)
h=g.replace(d,d+'-')
i=h.split('-')
j=[]
for base in i:
if (c and d) in base:
j.append(base)
elif (a and b) in base:
j.append(base)
try:
yy=str(pm)
op=open('Gene'+yy+'.fas','w')
op.writelines(yy+doc+'\n')
op.writelines(j[0])
op.close()
pm=pm+1
return