plz help
sandy smile
hi,
Thanks in advance.I am doing bioinformatics and plz help me
Consider a sequence
S='UACUGUUAA'
I have to split three as ‘UAC’,’UGU’,’UAA’
and Consider the position within the array element
0 1 2 0 1 2 0 1 2
U A C, U G U, U A A
And finding the frequency of occurrence of U,C,A,G in their respective position.so far i have identified the position .but i dont know to calculate the frequency.
Desired output:
Total number of U at 0 th position :3
Total number of U at 1th position:0
Total number of U at 2nd position:1
Total number of A at 0 th position :0
Total number of A at 1sth position:2
Total number of A at 2nd position:1
Total number of C at 0 th position :0
Total number of C at first position:0
Total number of C at second position:1
Total number of G at 0 th position :0
Total number of G at first position:1
Total number of G at second position:0
i have wrotten program upto this.please help.
program:
content='UACUGUUAA'
s=''
for i in range(0,(len(content))):
s=s+content[i].replace('\n','')
print len(s)
L=[]
for k in range(0,len(s),3):
two=s[k:k+3]
if len(two)==3:
L.append(two)
#L[k].find('A')
print len(L)
print L
for i in range(len(L)):
if L[i].find('A')>0:
b=L[i].index('A')
print i,'th element of A is in the position of',b
output:
9
3
['UAC', 'UGU', 'UAA']
0 th element of A is in the position of 1
2 th element of A is in the position of 1
Walker Hale IV
from pprint import pprint # only needed for some output below
seq = 'UACUGUUAA'
codons = [seq[k:k+3] for k in range(0, len(seq), 3)]
print codons
# totals[position][base] = count
totals = [
{'A': 0, 'C': 0, 'G': 0, 'U': 0},
{'A': 0, 'C': 0, 'G': 0, 'U': 0},
{'A': 0, 'C': 0, 'G': 0, 'U': 0}
]
for codon in codons:
for pos in range(3):
base = codon[pos]
totals[pos][base] += 1
pprint(totals)
for c in 'UACG':
for pos in range(3):
print 'Number of %s in position %d: %d' % (c, pos, totals[pos][c])
print
-Walker
> -~----------~----~----~----~------~----~------~--~---
>
>
--
Walker Hale <walker....@gmail.com>